Amy: *Upon evading E-100: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: "Dummies! Dummies! Dummies! 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.