1. Majin Boo (I'll call him Fat Boo) fights SSjin 2 Majin Vegeta, who was equal to SSjin 2 Goku, and crushes him. Vegeta resorts to self-destructing because he's so far below Boo and sees no other choice. We've got this so far:

Fat Boo > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 465 (DBZ 271), P7.1-2
Context: after Vegeta blasts a hole through Boo’s chest
Boo: “That hurt…a little bit…hehehe…”
Vegeta: “…Are you immortal?...”

Chapter: 466 (DBZ 272), P1.3
Context: after Boo’s big attack that makes a crater
Vegeta: “…Wh-what the?...Ridiculous; he’s st-strong, and to top it off immortal too…Damn it all…”

Chapter: 466 (DBZ 272), P2.3
Piccolo: “Even Ve-Vegeta absolutely can’t scratch that thing…”

Chapter: 467 (DBZ 273), P1.2-3
Trunks: “N-no! We’ll fight too! You’ll be killed on your own, papa! We’ll definitely be able to defeat him if we 3 do it together!”
Vegeta: “It’s no use…No matter how many of us go at him…Not if we fight in the ordinary way…”

Chapter: 469 (DBZ 275), P5.1
Piccolo: “Just as Kaioshin feared, Majin Boo’s strength surpasses our imagination…If we leave him alone like this, then without a doubt all life on not merely the Earth, but throughout the entire universe will be wiped out…”

Chapter: 469 (DBZ 275), P5.6-7
Goku: “Damn it! If either Vegeta or Gohan were alive, maybe we could have managed something…”
Piccolo: “…No, it probably wouldn’t matter how many people went at him…He wasn’t at that level…”

Chapter: 472 (DBZ 278), P10.7
Context: after Goten and Trunks question Goku’s power and Piccolo gets mad
Goku: “It’s alright, Piccolo…I really am weak. It don’t look like I can beat Majin Boo, not even a little bit.”

2. SSjin 3 Goku stalls Boo so Trunks can get the Dragon Radar. When Goku returns to the Lookout, he tells Piccolo he "probably" couldn't have beaten Boo. Piccolo is visibly skeptical, but for now, we've got this:

Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 476 (DBZ 282), P10.5-8
Piccolo: “Goku…There’s something I want to ask you while I’ve got the chance…[ ] …That Super Saiyan 3 thing earlier…if you had gone all-out, wouldn’t you have been able to defeat Majin Boo?...How about it, am I wrong?”
Goku: “Nah, I don’t know…When it comes to Majin Boo’s strength, it’s like a lie…I think that I probably couldn’t have won…”

3. Goku introduces Fusion and states twice that if the boys perfect it, they'll definitely be able to beat Boo. The boys could only go SSjin, so that's what Goku assumed they'd beat Boo with, otherwise he would have stated they could beat him even without the use of the form. Also, he tells Piccolo he told Boo a stronger fighter than him would come in 2 days; he never actually told this to Boo, but Piccolo doesn't know that. Now we have:

SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 472 (DBZ 278), P9.4
Context: after explaining that Fusion lasts 30 minutes
Goku: “With these two, if they just manage to perform Fusion successfully, I think they’ll definitely be able to defeat him within 30 minutes. Fusion is just that extreme.”

Chapter: 477 (DBZ 283), P11.8
Context: Chi-Chi thinks Goten will get killed by Boo
Goku: “Don’t worry. If he perfects the technique he’s trying now, he definitely ain’t gonna lose.”

4. Goku leaves and the boys finally get Fusion right. Gotenks forms in Base first, and right away Piccolo tells him he's not strong enough to even think about beating Boo. Gotenks cockily disobeys Piccolo and leaves to fight Boo, but returns after a prompt butt-kicking, cementing Piccolo's statement. The boys then fuse as SSjins, and Piccolo is in awe of SSjin Gotenks' power, but questions his speed; notice he doesn't question Gotenks' power. When Gotenks flies off and Piccolo finally catches up to him, Gotenks flaunts his speed and flies off again, but Piccolo shows no fear except that Gotenks only has 1 minute left to fight. Since nothing thus far contradicts it, we have:

SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 480 (DBZ 286), P11.4-5
Context: after Piccolo says to try Fusion again, as Super Saiyans
Gotenks: “Hehhehheh…Aren’t you underestimating me? Like this, I’m more than enough to defeat Majin Boo.”
Piccolo: “Yo-you idiot! What are you saying?! You don’t know anything about Majin Boo’s fearsomeness! No matter how incredible you may be, at that level there’s still absolutely no way you’d be able to win!”

Chapter: 480 (DBZ 286), P13.2-3
Context: after Gotenks returns from fighting Boo
Gotenks: “I got the tar beaten out of me…”
Piccolo: “Alright, your fight with Majin Boo is 1 day from now! Until then, train as much as you can! If you get even a little bit stronger, it will be more effective when you perform Fusion. Got that, you miserable little punks?!”

Chapter: 482 (DBZ 288), P7.2-3
Context: after Super Saiyan Gotenks forms for the first time
Piccolo: “…Yeah…Your ki really is absolutely incredible, but how about your movement?...Show me a little”
Gotenks: “Is that alright? If I show you here, the house might break. I’ll do it on the ground.”

Chapter: 482 (DBZ 288), P9.3-8
Context: Piccolo finally catches up to Gotenks
Gotenks: “You’re slow. So you finally got here? Besides circling around the Earth several times, I even took a little afternoon nap. [ ] Fuffuffuh…So you can’t tell just from my speed just now? My super-duper incredible power…! …Which is to say that the test is over, and I’m going to go take care of that annoying Majin Boo right away…”
*Gotenks takes off*
Piccolo: “H-hey, you idiot! Kuh…! Wh-what a *****head…H-he already has only 1 minute left that he can stay merged. That dimwhit…!”

5. Super Boo forms and Piccolo immediately rushes the boys into the Room of Spirit and Time, telling Krillin that they can't win as they are now. He also states Super Boo is superior to Fat Boo in all aspects, including strength. We have:

Super Boo > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 487 (DBZ 293), P13.5
Context: as Piccolo plans on having Goten and Trunks train in the Room of Spirit and Time
Piccolo: “Can’t you tell…?! As they are now, even if they perform Fusion they can’t win, no doubt about it…! Tell them that if they don’t want to die while they’re still just little brats, then they should train as much as they can…!”

Chapter: 488 (DBZ 294), P5.5-6
Trunks: “Huh!? That’s Majin Boo!?”
Goten: “He-he really has changed…”
Piccolo: “It’s not just his appearance…Everything about him is definitely greater than before…”

6. The boys train for about 15 days if I remember correctly. While still training, Trunks states that even with "regular Fusion", they should be able to beat Boo. When Base Gotenks actually forms, Piccolo thinks they might have a chance. Logic be damned, this puts Base Gotenks above his previous SSjin power by a decent margin at least.

Super Boo ~ Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 489 (DBZ 295), P3.5
Context: Trunks doesn’t like the idea of fighting Boo as a Super Saiyan 3 from the start
Trunks: “I think…that we’ve already progressed so much that even in a regular state Fusion, we’ll be about equal with Majin Boo...”

Chapter: 489 (DBZ 295), P11.5
Context: seeing Gotenks after he’d trained in the Room of Spirit and Time
Piccolo: “He-he really is different…! He really has greatly powered up…! Th-this just might…!”

7. It turns out Goku was right that Boo's chi was "like a lie", and Base Gotenks is promptly shoveled off the pavement after being humiliated; so Super Boo was heavily underestimated. It takes SSjin 3 for Gotenks to actually damage Boo. Near the end of their fight, it appears as if Gotenks is about to finish Boo, but time runs out and he splits back into Goten and Trunks. Super Boo later states to Gohan that he felt Gohan's chi on the Kai planet and decided to wait for him. For simplicity's sake, we'll put Gotenks and Boo on par with each other, so we have:

SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 495 (DBZ 301), P6.1-3, P7.1-3
Context: after Gotenks blasts Boo with the Rapid-Fire Die-Die Missiles and Piccolo stops him
Gotenks: “Well, whatever. I already did quite a lot, after all. He should be pretty weakened.”
*Boo comes out*
Gotenks: “…He ain’t weakened…This really pisses me off!”
Piccolo: “N-no…He is weakened…I don’t know about physically, but he’s weakened a little mentally…! Th-this is the first time…that he’s fought someone strong like you…He’s feeling flustered by someone whose strength is at least on par with his own…”
Gotenks: “Dehhehheh! So in other words, Majin Boo’s freaked out, huh!? That’s right! My strength ain’t half-assed! I’m the best in the universe!”
Piccolo: “Don’t let your guard down! He’ll be coming at you frantically now…!”
Gotenks: “Dahhahhah, that’s problem, no problem at all! That’s just what I was hoping for!”

Chapter: 499 (DBZ 305), P12.2-4
Gohan: “…That was dirty, you bastard…You ingested the two of them into yourself…”
Boo: “It’s your fault. You were stronger than I, who should have been the absolute strongest…When I sensed your distant presence, I started up on this strategy…In case maybe, just maybe, there was anyone stronger than myself…Then I hit upon it: if I absorbed that ‘Super Gotenks’ squirt I was fighting at the time, then no matter what kind of guy appeared, my throne as the strongest would not be shaken…”

8. Gohan, his potential freshly released thanks to Elder Kaioshin, ends up whooping Boo's candy ***** all over the tri-state area, so Boo self-destructs and the fun begins, giving us this:

Ultimate Gohan > SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 498 (DBZ 304), P1.3, P2.4
Context: after Gohan beats up on Boo
Gohan: “You can’t win…”
[ ]
Gohan: “I see…So you tried testing your power just to be sure, and I really was above you…That’s too bad, Majin Boo.”

Chapter: 498 (DBZ 304), P3.2
Context: Boo says he’ll kill Gohan
Gohan: “You’re the one who should best know just how impossible that is…”

Chapter: 498 (DBZ 304), P7.4
Context: after Boo disappears
Trunks: “Even if he really is still alive, it doesn’t matter! That jerk was helpless against Gohan!”

9. Boo absorbs SSjin 3 Gotenks and Piccolo (I'll call him Gotenks-Boo), and proves himself quite superior to Gohan. Another important tidbit is that he states himself to be the most powerful Boo to date. We now have this:

Gotenks-Boo > Ultimate Gohan > SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 499 (DBZ 305), P11.1
Boo: “…What do you think, Gohan? My strategy succeeded safely. Look, isn’t it magnificent? This is a moment that will never appear again, no matter what the future may hold: the birth of the strongest majin.”

Chapter: 500 (DBZ 306), P6.4, P7.1
Context: after Gohan and Boo fight a bit
Boo: “What’s the matter? You’re erasing your ki and hiding in a place like that…Are you trying to stall for time? Meaning that just from that you seem to have realized…That like this, you’re absolutely no match for me…”

Chapter: 501 (DBZ 307), P5.5
Context: Elder Kaioshin warning Goku about recklessly going to rescue Gohan from Gotenks-absorbed Boo
Elder Kaioshin: “I hate to say it, but I don’t think you could win against this current Majin Boo even if the two of you went at him together…”

Chapter: 502 (DBZ 308), P5.6
Boo: “…What, did you plan on coming to save everyone? You idiot…Can’t you tell that I’m in a fundamentally different dimension than the Majin Boo from back then?”

Chapter: 502 (DBZ 308), P7.1
Context: talking to Goku after knocking out Tenshinhan
Boo: “…That guy just now was apparently quite a master, but he was reduced to that state in just 1 one kick…You’re making some worthless boasts…Frankly, no matter what you try, you absolutely won’t be able to even inflict damage on me.”

10. Gotenks defuses inside Boo (Piccolo-Boo for me), reducing his power so much that now Gohan can beat him again. We have:

Gotenks-Boo > Ultimate Gohan > Piccolo-Boo >/< SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 502 (DBZ 308), P10.4-5
Goku: “Hahha—ah! Piccolo’s coming out strong now! Looks like the Fused squirts have returned to normal! You ran out of time! Tooo—oo bad! Your power’s fallen a whole lot. Cheh…I’m a little disappointed. This way, Gohan will be able to beat you even on his own…”

11. Boo absorbs Gohan (Gohan-Boo) and leaves Goku sweating multiple oceans. Once again, Boo states himself to be the most powerful Boo to date, so we get:

Gohan-Boo > Gotenks-Boo > Ultimate Gohan > Piccolo-Boo >/< SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 502 (DBZ 308), P13.1
Boo: “Fu…fuhahahaha…! This is great! I’ve powered up even more than before! And what’s more, now there’s no time limit!”

Chapter: 506 (DBZ 312), P2.5-6
Context: after Boo absorbs Vegetto
Elder Kaioshin: “…Don’t you think it’s a little strange? …Each time Majin Boo has absorbed a warrior up to now, his power has gone up and his appearance has changed…But this time…”
Kaioshin: “He hasn’t cha-changed…! Wh-what’s that mean!?”
Note: as we soon learn, Vegetto’s barrier prevented him from being truly absorbed.

Chapter: 506 (DBZ 312), P3.5
Context: after Boo ‘absorbs’ Vegetto but nothing happens
Boo: “Hmm…Well, at any rate, I absorbed him. I have now become the strongest majin; without a doubt, there is nobody throughout the various worlds who compares to me…That’s fine…”

12. Goku and Vegeta use the Potara earrings to make Vegetto, who practically crucifies Boo, giving us this:

SSjin Vegetto > Gohan-Boo > Gotenks-Boo > Ultimate Gohan > Piccolo-Boo >/< SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 504 (DBZ 310), P9.2-3
Context: as Vegetto beats up on Boo
Kaioshin-Kibito: “H-he’s strong!!! Majin Boo there is helpless!!! To think that merging with the Potara would be this incredible…!!”
Elder Kaioshin: “Idiot, it’s because it was those two that they were able to go so far. Two of the top 3 masters in both the living world and afterlife have merged, after all. What’s more, two rivals have joined together. That’s definitely strongest.”

Chapter: 505 (DBZ 311), P1.2
Context: after Vegetto outclasses Boo
Vegetto: “…Well, don’t feel too bad. Even I’m surprised. To think that I’d be able to make this big a fool out of you.”

Chapter: 505 (DBZ 311), P5.2
Context: after Vegetto destroys the Super Ghost Kamikaze Attack
Vegetto: “Did you really think that kind of technique would work on me? A child thought that technique up. You’re pretty desperate, aren’t you?”

Chapter: 505 (DBZ 311), P6.6
Context: Vegetto blocks Boo’s attacks with his legs
Vegetto: “Hey, hey! What’s the matter!? My legs alone are more than enough to deal with the likes of you!”

Chapter: 505 (DBZ 311), P9.5-6
Context: after Boo turns Vegetto into a candy ball, and candy-Vegetto promptly hits him
Vegetto: “Sorry, my bad. Unfortunately for you Boo, it seems that somehow my strength hasn’t changed, despite me turning into this. What will you do? Your opponent is the world’s strongest candy ball! This is bad for you, isn’t it? I’m so small that it’s hard to attack me.”

13. Goku and Vegeta defuse inside Boo. They detach the boys and Piccolo from inside Boo and Vegeta wants to blast his way out, but Goku quickly tells him that they're no match even for normal Super Boo. Nothing's changed from before, so we still have this:

SSjin Vegetto > Gohan-Boo > Gotenks-Boo > Ultimate Gohan > Piccolo-Boo >/< SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 506 (DBZ 312), P12.4-5
Context: after Goku and Vegeta revert Boo back to regular evil Boo
Goku: “Hehhe~~eh! With this, Boo’s power should have fallen significantly! We’re almost there! See, see: the size of his ki is completely different than before!”
Vegeta: “Alright! Let’s blast out of here and escape!”
Goku: “Wait! Even though Boo has returned to normal a whole lot, we’re still simply no match for his strength! If we go outside like this, we’ll definitely be done in…!”

Chapter: 507 (DBZ 313), P2.4-5
Context: after evil Boo appears inside his own body
Vegeta: “Da…damn it…! Th-this could be bad…”
Goku: “Di-didn’t I tell ya to wear your Potara?! Th-this is why! If we could just go outside and merge, then this kind of guy would be an easy victory!”

14. They manage to get out of Boo's body after detaching the innocent Boo (Good Boo), which transforms Super Boo into a buff version of himself (Buff Boo). Goku questions if his chi is increasing, so we have this:

SSjin Vegetto > Gohan-Boo > Gotenks-Boo > Ultimate Gohan > Buff Boo > Piccolo-Boo >/< SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 507 (DBZ 313), P13.5
Context: as evil Boo reverts to his South Kaioshin form
Goku: “H-hey…Vegeta…His ki is increasing, ain’t it…!?”

15. Buff Boo continues transforming and reverts to the original Boo, Kid Boo. Vegeta makes a comment on Boo's size, and Goku rejoices that they've "done it", which in context means they've weakened Boo. Since they were deciding on who would fight Boo first on the Kai planet, this points to Boo being below even SSjin 2 Vegeta's level; if Boo was emitting power on par with a SSjin 3, I doubt Vegeta would have any qualms letting Goku go first. So we have this:

SSjin Vegetto > Gohan-Boo > Gotenks-Boo > Ultimate Gohan > Buff Boo > Piccolo-Boo >/< SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > Fat Boo > SSjin 3 Goku > SSjin 2 Majin Vegeta/Goku > Kid Boo

Supporting Quotes
Chapter: 508 (DBZ 314), P3.4-6
Context: after Boo reverts to his pure form
Goku: “…”
Vegeta: “……Heh…Heheheh…Look! He’s shrunk down quite a bit!”
Goku: “We did it! This way, we might be able to manage something.”
Context: ‘He’s shrunk’ refers to Boo’s body, not his ki.

Chapter: 509 (DBZ 315), P6.8, P7.1-5
Context: after Kaioshin hands Goku his Potara but he refuses it
Goku: “…Like I thought, these…just ain’t suited for us…Even though you went out of your way to hand ‘em over…We want to fight with only our own power. I’m sorry, especially since things are so dangerous now…But he ain’t merged anymore either…“
Elder Kaioshin: “Yo-you idiot! What are you saying?! And at a time like this! It’s not like you gu-guys are in a martial arts match with Boo, you know!”
Vegeta: “…Well said, Kakarot. Just like a true…Saiyan.”
Kaioshins: “…!”
Goku: “It’s alright. I’m tellin’ ya, don’t worry. He can’t come all the way here. We’ll think up some sorta strategy. I feel bad for the aliens who will be sacrificed in the meantime, but we’ll use the dragonballs later…”

Chapter: 509 (DBZ 315), P10.2
Context: as Goku and Vegeta prepare to fight pure Boo
Elder Kaioshin: “Fr-from the looks of it, they don’t intend to perform Fusion either…Shi-*****…! Saiyans are so troublesome…!”

Chapter: 509 (DBZ 315), P11.3
Context: as Goku and Vegeta play rock-paper-scissors to decide who fights Boo
Elder Kaioshin: “Th-those dimwits! Th-they intend to fight one at a time?! They’re not gonna fight together?!”

16. Goku wins the game and faces Boo first. He transforms right to SSjin 3 and a nigh-equal battle unfolds between the two (the anime goes crazy with the filler in this battle). Goku stops for a moment and Vegeta tells him that at full power, he should be able to completely obliterate Boo. Goku says he's been trying but hasn't had the chance yet. He also states he could've beaten Fat Boo but chose not to, giving us this:

SSjin Vegetto > Gohan-Boo > Gotenks-Boo > Ultimate Gohan > Buff Boo > Piccolo-Boo >/< SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > SSjin 3 Goku > Kid Boo > Fat Boo > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 509 (DBZ 315), P11.4-6
Context: as Goku prepares to fight Boo
Goku: “Alrii~~iight. I’d better go all out right from the start…! If we get done in, then the entire universe will go ‘poof’…”
Vegeta: “Let me see this ‘Super Saiyan 3’ thing with my own eyes…”
Goku: “Is that alright? You just might not get your turn…I can say this now, but the truth is that with that fat Boo, I would have been able to defeat him at the time with Super Saiyan 3…However, I wanted the young guys to manage something…For the Earth’s sake too…”

Chapter: 510 (DBZ 316), P13.1-6
Vegeta: “Don’t hesitate for my sake, and finish him off! With that Super Saiyan 3, you should be able to completely wipe out Boo with your ki once you gather it with all your might…!”
Goku: “Ye…yeah…I’ve been thinking of doing that as well since awhile back, but…I haven’t gotten the chance.”
Vegeta: “Eh?”
Goku: “If I want to wipe him out, I gotta gather ki for about one minute.”
Vegeta: “One minute?!”
Goku: “Dammnit~~~If it was with the Potara, I could have done it in one blast. …..Cheh~~~I guess I went and showed off too much. But I thought things would go a little better than this…!”
Vegeta: “…S …So you weren’t thinking of me…”

17. Goku begins charging up and Vegeta faces Boo, but gets squashed without even hitting Boo once. As Boo is about to hurt Mr. Satan, he stops and spits out Good Boo. The two fight and even though Good Boo quickly becomes a rag doll, he does better and lasts longer than Vegeta did, even considering his regeneration powers which were going down since he was fighting another Boo. This also gives us a good place for Skinny Boo (the gray one), since he was stated to be stronger than Good Boo but couldn't be stronger than Fat Boo, giving us this:

SSjin Vegetto > Gohan-Boo > Gotenks-Boo > Ultimate Gohan > Buff Boo > Piccolo-Boo >/< SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > SSjin 3 Goku > Kid Boo > Fat Boo > Skinny Boo > Good Boo > SSjin 2 Majin Vegeta/Goku

Supporting Quotes
Chapter: 485 (DBZ 291), P2.3
Narrator: “Due to his strong anger, the evil portion that Majin Boo had kept inside himself greatly swelled up and became another Majin Boo, who came flying out…In other words, he was divided into a pure evil Majin Boo and an innocent Majin Boo…”

Chapter: 485 (DBZ 291), P7.4
Context: as the two Boos fight
Narrator: “The original Majin Boo had no chance of winning...This was because during the split, the majority of the power went to the evil one…"

Chapter: 512 (DBZ 318), P12.4
Context: after good Boo fights pure Boo a little
Good Boo: “…Uh oh…I kinda can’t win…”

Chapter: 513 (DBZ 319), P6.1
Context: as pure Boo beats up on good Boo
Goku: “Th-this is bad…this way it’s only a matter of time before he’s done in…”

Chapter: 514 (DBZ 320), P5.3
Context: as pure Boo beats up on good Boo some more
Vegeta: “…This is bad…Have you noticed, Kakarot?...The fatso’s power is falling…If it’s Boo against Boo, then he could take damage…”

Chapter: 515 (DBZ 321), P3.1
Context: as pure Boo continues to beat up on good Boo
Vegeta: “*****…! Th-this is bad! The fat one is on the brink of death…”

18. Goku finally completes the Genki-Dama and fires it, but because of his diminished stamina, Kid Boo is able to hold it back. Once Goku's stamina is restored by Porunga, he's able to push the attack and finish off Boo for good. All in all, we end up with this:

SSjin Vegetto > Gohan-Boo > Gotenks-Boo > Ultimate Gohan > Buff Boo > Piccolo-Boo >/< SSjin 3 Gotenks >/< Super Boo > SSjin Gotenks (post-RST) > Base Gotenks (post-RST) > SSjin Gotenks > SSjin 3 Goku > Kid Boo > Fat Boo > Skinny Boo > Good Boo > SSjin 2 Majin Vegeta/Goku

So if you followed along, considered the quotes, and have read the manga and didn't rely on the self-contradicting anime, then this is roughly what you would come up with. Some points people debate, like Base Gotenks' strength post-RST, but overall, most people that use the manga for debates come up with something very similar to this lineup. I'll go even further and address some of the points I know Kid Boo > Super Boo believers will most likely bring up.

1. Inside Boo, Goku was lying to Vegeta and wanted to fuse because he didn't want to upset Vegeta with SSjin 3, was afraid the strain from the form would weaken him too quickly to win the fight, and was also afraid he would remain the size of a flea. That and he didn't want to fight too hard, so he wanted an easy victory.

Counter-argument
a. While this is somewhat true, Goku wouldn't let himself die just to protect his friend's pride. 7 years prior on the Lookout, he blatantly told Vegeta that he was a lot stronger than him, knowing it would piss him off. Even during the Boo arc, although he didn't use the form in their fight for a few interpretive reasons, it doesn't necessarily mean he was protecting Vegeta's pride. He was trying to get Vegeta to fight alongside him and Gohan under the false pretense that they could win. During the fight with Kid Boo, Vegeta tells Goku to stop messing around and finish Boo off, and Goku basically tells him, "Man, I've been trying, but I haven't gotten the chance", effectively rendering Vegeta's understandably selfish view invalid and proving that Goku would use the form to its fullest if he really had to, despite Vegeta being right there to witness it; Vegeta even says "So he wasn't thinking about me...", backing this up.

Chapter: 510 (DBZ 316), P13.1-6
Vegeta: “Don’t hesitate for my sake, and finish him off! With that Super Saiyan 3, you should be able to completely wipe out Boo with your ki once you gather it with all your might…!”
Goku: “Ye…yeah…I’ve been thinking of doing that as well since awhile back, but…I haven’t gotten the chance.”
Vegeta: “Eh?”
Goku: “If I want to wipe him out, I gotta gather ki for about one minute.”
Vegeta: “One minute?!”
Goku: “Dammnit~~~If it was with the Potara, I could have done it in one blast. …..Cheh~~~I guess I went and showed off too much. But I thought things would go a little better than this…!”
Vegeta: “…S …So you weren’t thinking of me…”

b. Goku had no clue about the strain of the form in a living body until he was well into the fight with Kid Boo.

Chapter: 513 (DBZ 319), P1.2
Context: after Goku drops out of Super Saiyan 3
Goku: “Da-dammit…When I was dead, it was no problem at all…It seems that in the end, becoming a Super Saiyan 3 with a living body eats up an excessive amount of ki…”

c. There's absolutely no indication Goku thought he'd remain small if he left Boo's body. The whole context of the happenings inside Boo was that without any type of fusion, they were doomed.

d. This is really unfounded and has no evidence to back it up. Goku states Boo would kill him even with Vegeta's help as long as they weren't merged.

2. Gohan's chi wasn't enough so Kid Boo can't possibly be weaker than Super Boo.

Counter-argument
a. Gohan didn't donate all of his chi, shown by how he's not winded like the earthlings. Goten and Trunks didn't fuse into Gotenks or even turn Super Saiyan, so why would Gohan be giving all of his chi? It wouldn't make any sense. The Genki-Dama also collects genki, which is just one part of three of raw ki (I juggle between "chi" and "ki", but it's the same thing), as stated by Toriyama in the SEG: Story Volume.

Q. What's the trick to winning battles [in the DB world]?

A. Toriyama says it all comes down to 'ki', the size of it and the ability to control it. He says it includes several forms: genki, yuuki & shouki (energy, bravery & true character). You can only train your muscles to a certain point, it's 'ki' that carries you beyond that and what helped Goku come closer to being the strongest warrior in the universe.

3. Kid Boo was totally toying around with Goku.

Counter-argument
a. There's nothing to prove this as true. Nothing says Boo wasn't fighting at his fullest against Goku. Why would he slap Vegeta and Good Boo around but fight so evenly with Goku? He's a mindless monster, but even then it still doesn't make sense. He still has instincts, and when you're in trouble, you fight your hardest (usually), which is what Kid Boo did. He was never in any danger with Vegeta or Good Boo, but Goku actually challenged his livelihood.

b. Boo holding back the Genki-Dama is in no way proof that he was stronger than Goku. It's made a point that Goku can't fire the Genki-Dama correctly because of his failing stamina.

4. Both South Kaioshin and Dai Kaioshin weakened Boo, so when they were taken away, Boo returned to his most powerful state.

Counter-argument
a. This is completely false, and most likely brought about by the anime, and Viz's translation doesn't help. In the original Japanese, after Kibitoshin explains Boo's past, Elder Kaioshin ascertains that the he was finally complete and that Kid Boo is the most troublesome one. Kibitoshin then says that the heart he gained by lowering his power through absorption has returned to the way it was. Daizenshuu #7 states that only Dai Kaioshin weakened Boo. Most Kid Boo supporters dismiss the daizenshuu entry as just "guidebook crap", and dismiss the original Japanese translation as just "another fan translation" and say that Viz is the only good translation because it's official. In the Viz translation, Elder Kaioshin states that the "souls [Boo] ate tamed him", which is easy for Kid Boo supporters to say proves that both the Kais weakened Boo. But this isn't so, because even if the Japanese translation is translated by a fan, it's a direct translation, and not an "adaptation" like the Viz translation, so it is more accurate, whether the Kid Boo supporters want to accept that or not.

5. Kibitoshin states Kid Boo is the most powerful Boo, so it's true.

Counter-argument
a. This is a case of people taking the anime's word over the manga's. In the anime, Kibitoshin, Goku, and the narrator all state Kid Boo is the strongest, at least in the original Japanese version. Of course in the manga, nobody says this because Boo is just the most troublesome one there. With the anime, trying to make Kid Boo the strongest leads to a lot of headaches. In the manga, it's very simple to place Kid Boo without having to twist statements around.

b. Gotenks-Boo states he is the most powerful Majin to date. He has memories of his past, so it'd be a foolish mistake to say he doesn't remember being Kid Boo. Gohan-Boo also states he has become the strongest Majin, so both of them are stronger than Kid Boo by their own admission.

6. Goku was going to help Gohan fight Gotenks-Boo, so he has to be stronger than Super Boo.

Counter-argument
a. Goku acted recklessly because his son was in danger. Elder Kaioshin tells him that he can't beat Boo even he and Gohan fought together, and Goku admits he's right, and then brings up Fusion as an option.

Chapter: 501 (DBZ 307), P5.5
Context: Elder Kaioshin warning Goku about recklessly going to rescue Gohan from Gotenks-absorbed Boo
Elder Kaioshin: “I hate to say it, but I don’t think you could win against this current Majin Boo even if the two of you went at him together…”

Vizbig, vol.9, pg.216
Goku: "Then I'm off!"
Elder Kaioshin: "Son Goku! Wait!!"
Goku: "Huh?!"
Elder Kaioshin: "How do you plan to beat Boo? I don't think the two of you together could do it."
Goku: "...Uh...um...uh...I know!! Fusion!! Gohan and I will fuse!!"

7. Goku fought Gotenks-Boo and did better than Gohan.

Counter-argument
a. This is anime filler. Goku never fought Gotenks-Boo in the manga, and was sweating when Boo charged him. Even in the anime, Goku couldn't get a single hit on Boo except for one chi blast when Boo was distracted, while Gohan was able to fight evenly with Boo in the beginning of their fight.

8. Goku is stronger than Gotenks so he has to be stronger than Super Boo. Toriyama even said it in an interview!

Counter-argument
a. First off, Toriyama never said such a thing. That was a fake interview made up by some fan. Any Japanese fan will tell you how fake that interview is.

b. Goku stated Gotenks would be stronger than him and it's never contradicted, so it remains true. Even if Goku was stronger than Gotenks, Gotenks trained in the RST and grew immensely stronger, and would have undoubtedly surpassed Goku in power.

9. Goku wanted to bring both Gohan and Gotenks to fight Boo, so obviously he didn't think just Gohan could do it.

Counter-argument
a. It was more of a first-thought thing; he's stating ideas off the top of his head. Listing them both was more of a precaution in case one got absorbed again.

10. Vegeta states that Goku is the only one that can fight Kid Boo, so that must mean Goku and Kid Boo are the strongest ever.

Counter-argument
a. Vegeta does say this, but the context shouldn't be ignored. He'd never seen or sensed Gotenks and Gohan, so he wouldn't know how powerful they are.

11. After the final battle, Vegeta asks Goku what they would do if Good Boo spit out another "one of those monsters", and Goku says they would train hard so they can't be beat. This must mean Kid Boo was stronger than all of them.

Counter-argument
a. In reality, Vegeta asked what they'd do if Boo birthed another "evil Boo" (Viz changes it to the monster line), who the English-speaking community knows as Super Boo. Gohan fought Super Boo and technically lost because he was absorbed, so what would stop that from happening a second time? That's something Vegeta didn't want happening again, since he wouldn't fuse with Goku again.