Below is probably every line that can tell us something about the difference between SS3 Gotenks & SS3 Goku. Tell me if I missed anything.
Chapter: 472 (DBZ 278), P9.4
Context: after explaining that Fusion lasts 30 minutes
Goku: “With these two [Goten and Trunks], if they just manage to perform Fusion successfully, I think they’ll definitely be able to defeat [Boo] 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.”
Goku predicts that SS Gotenks would be strong enough to kill Innocent Boo. Since there is no way to know for sure, it is possible that he could be wrong, but since Goku is a very experienced fighter, and also knows how powerful Fusion is, SS Gotenks has to be not very far from Innocent Boo, even if he is weaker than him.
Chapter: 476 (DBZ 282), P10.5-8, P11.1-3
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…”
Piccolo: “…Probably? Knowing you, why didn’t you try until the very end?...Does it have to do with that energy…?”
Goku: “No…I’m no longer a human who’s particularly even supposed to be here…I shouldn’t be the one to do it. It’d be better for these young guys to solve things somehow or another…After all, some other outrageous guy might show up eventually, right? …It's a nasty gamble, but…Seeing those two super-gifted squirts, it made me want to take this gamble…”
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…”
Goku says that he probably wouldn't be able able to kill Innocent Boo, but later admits that he lied. Which means that it is still unclear if SS Gotenks is stronger or weaker than SS3 Goku, but we know that they are not too far in power.
Goku also confirms that Boo has a strange ki that is difficult to measure.
Chapter: 487 (DBZ 293), P13.4-5
Context: after evil Boo shows up and demands to fight Gotenks
Piccolo: “Go hit Trunks and Goten to wake them up, and take them into the Room of Spirit and Time…! Even in just 1 hour, they’ll be able to do 15 days worth of training.”
Kuririn: “Heh!? If we do it now…”
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…”
Piccolo believed that SS Gotenks had no chance only when Boo turned into Evil Boo, which means that SS Gotenks
may had a chance against Innocent 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…!”
Piccolo sensed that Gotenks had gotten much stronger, but we still don't know if SS Gotenks is stronger or weaker than SS3 Goku. However, Gotenks turns Super Saiyan 3, which makes him 8 times stronger. We do know that SS Gotenks is much stronger than SS2 Goku, so SS3 Gotenks must be stronger than SS3 Goku as well.
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 no problem, no problem at all! That’s just what I was hoping for!”
Chapter: 495 (DBZ 301), P13.3-
Context: as Gotenks beats up on Boo
Goku: “Amazin’, amazin’! At this rate, Gohan ain’t gonna get a turn!”
Kaioshin: “Oh!”
SS3 Gotenks shows power great enough to kill Evil Boo... if he had more time.
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 your 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!”
Goku is scared of Evil Boo. He believes that he & Vegeta together wouldn't stand a chance against him if they were to go outside, except if the could use the Potara to merge. You could say that Goku was lying so that he wouldn't hurt Vegeta's pride by showing SS3, but he had no problem of going full power against Pure Boo later, not to mention that merging with Vegeta forever just to not hurt his pride would be too stupid, even for Goku.
Chapter: 507 (DBZ 313), P4.2-4, P6.3-6
Context: as Goku and Vegeta are attacked by evil Boo
Goku: “Alrii—iight! Come at me if you’re gonna. I’ll open up a huge hole inside your body! *Boo smiles* Wh-what are you smiling about?...Do you think I can’t open one?”
Boo: “It’s no use.”
Goku: “Don’t underestimate me.”
*Goku blasts, not much happens*
Goku: “…”
Vegeta: “…It di-didn’t have any effect…”
Boo: “It stung a little here *points at head*, that’s all. You guys are now far, far smaller than fleas.”
Goku: “…So we’ve got no choice but to defeat you and then search for an exit somewhere.”
Boo: “No, you can’t defeat me. Not the way you guys are now…You’re gonna die, not me…”
So, while Goku was wetting his pants before, he acts cocky now. He is obviously bluffing, and believes he can open a hole in Boo's body because his body is like a gum. But Boo tells them that now that they have gotten smaller, they have gotten weaker as well.
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…!?”
Evil Boo transforms into S. Kaioshin Boo, which makes him even stronger than before, and also makes Goku even more scared.
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.”
Note: "He’s shrunk" is chidzimu, which typically refers to physical shrinking (like with Bulma's Micro Band) and throughout DB is never used to refer to ki diminishing. So Vegeta's probably talking about how Boo’s body has shrunk. That doesn't mean Boo's ki didn't go down too, but it's not what Vegeta's talking about here.
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 [Boo] 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…”
However, as S. Kaioshin Boo reverts back to Pure Boo, Goku is happy, and believes that they have a chance now, unlike against Evil Boo & S. Kaioshin Boo. He even refused the Potara, while he was strongly suggesting them against Evil Boo.
Chapter: 510 (DBZ 316), P8.2
Context: as Goku fights pure Boo
Vegeta: “Kakarot…You’re incredible…I am simply no match for that Majin Boo…You’re the only one capable of fighting him…”
Vegeta's whole "You are #1, Kakarotto!" doesn't mean that Goku is the strongest guy ever. He finally admits that between the two of them, Goku is the strongest, and the only one of the two capable of fighting Boo.
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…”
Both Goku & Vegeta confirm that SS3 Goku in full power can kill Pure Boo.
Chapter: 514 (DBZ 320), P7.4
Context: after Vegeta has the Earth brought back with the dragonballs
Goku: “Oh, I know! You’ll bring Gohan and Gotenks back to life so they can fight.”
Vegeta: “No.”
Just because Goku says this doesn't mean that Gohan & Gotenks have to fight together against Pure Boo. It could be read like that, but there are other lines before that that prove otherwise.
So, in the end, we know that Ultimate Gohan is stronger than SS3 Gotenks, who is stronger than Evil Boo, who is stronger than SS3 Goku, who is stronger than Pure Boo, who is stronger than Innocent Boo, who could be either stronger, or weaker (but without a big difference) than SS Gotenks, who is stronger than SS Goku, which makes SS3 Gotenks stronger than SS3 Goku, and Ultimate Gohan even stronger than those two.
