- When Eggman transforms his airship to make it more difficult to get to the bridge:
Tails: Wow! It just transformed! Did you see that?Sonic: [Gives Tails the biggest Captain Obvious look ever] Now how do we get to the bridge?Tails: I hate it when he doesn't listen.
- Gammas reaction after seeing the horror of his brother being torn apart and rebuilt into a new body.
- Gamma: (beat) This is the wrong room.
- Right before landing or rather, crash-landing on the Egg Carrier:
Tails: Alrighty! We're in!Sonic: We gotta land on the Egg Carrier.Sonic: What's that?Sonic: WHAT?!
- The scene becomes even funnier if you have the voice acting set to Japanese.
- After clearing Final Egg with Amy:
Amy: [Upon evading Zero after Final Egg] PHEW! That was close! [Face slowly forms the most miserable and horrified expression possible before abruptly snapping back to stoic]
- When Big the Cat leaves the sewer via elevator, the doors would close on his tail, prompting him to go "Ow".
- When Gamma is transported to the past in a vision, it is unable to determine its location, and states "This presents a problem." It's the delivery of the line that makes it funny.
- Similarly, Gamma demanding Amy that she "give him the bird." Of course, he means the bird she is carrying, but "the bird" is American slang for a very obscene gesture, which makes this scene look hilarious when looked in this context.
- Everyone's faces in general when speaking. It seems Sonic Team wasn't too good at rigging.
- For a bit of Black Comedy, one line: "All's well that ends well, right?" Well, yes, but the city is still quite flooded, and the bursts of water happened so suddenly that there's no way there aren't massive casualties to go with the universal property damage. GameboyHero/BrokenGameboys made a point of editing in, right after Tails said that, part of an earlier cutscene which shows water pouring out of buildings.
- Similarly, knowing the Super Sonic story in full, talk to the manager before triggering the cutscene that leads into the final boss fight. He'll say that he's sure the place will fill up.
- During the Chaos 0 fight, one of the cops moonwalks away from Chaos, still with gun trained on it.
- Eggman's tantrum after he thinks his robots failed to get Froggy-
Eggman: AAAAAARGH! DummiesDummiesDummiesDummies DUMMIES! None of you got the right one!
- After Sonic awakes from the flashback, he told Tails that he was on a snooze cruize. The scene pictures Tails with a very confused look.
- During Gamma's story, go walk around Station Square and talk to people. Really, the funniest part of this is just how few people seem to notice that you're anything unusual and will just launch into talking to you about their mundane problems and stuff. There are a few who notice, of course, and they may or may not be afraid, thinking you anything from a government enforcer to an eccentric rich man's servant robot to a costume (okay, that one's in Mystic Ruins) to knowing who your master is or was.
- Believe it or not, the fastest way to clear Amy's action stages is to have her hop like a bunny the whole way!
- Amy and Sonic are attacked by Zero, and just as Sonic prepares to battle the robot, Amy's sudden cry distracts him. His reaction says it all.
Amy: Woah!Sonic: Oh, now what?
- A little bit of Hilarious in Hindsight occurs in Gamma's story. When he gets transported to the past, Tikal tells him that the Chao are being protected by Chaos, describing him as a very "gentle and loving creature." Fast-forward to the end of the game, where Perfect Chaos is destroying everything in his path, potentially murdering thousands of innocent people. Gentle and loving indeed.
- Big the Cat's appearance in Tails' storyline is very random - charging towards Tails like he is going to run him over, only to trip and fall down. Froggy, who is being held by Tails, hops away and Big runs after him. Tails views the experience as a Big Lipped Alligator Moment.
- Station Square's police force pulling a Screw This, I'm Outta Here! when they realize their guns have no affect on Chaos' weakest form.
Officer: Oh no! Our weapons are useless! Retreat! All personnel, fall back!
- Big the Cat's boss battle with Chaos 6 is hilariously anticlimactic, especially after all the hell that fishing for Froggy has been before. He can pull Froggy out in an instant.
- At one point in Amy's Hot Shelter, you go into a restroom. With multiple stalls. Apparently, even Eggman's all-robot henchmen crew needs to use the facilities too.