* What's Team Chaotix's solution to a technical problem? [[PercussiveMaintenance Smash the computer!]] Believe it or not, it works every time.
* This moment:
-->'''GUN Soldier''': Hey? Where's my bike? Has anyone seen where it i-- ''(Shadow runs him over with a motorcycle)''
* When you've run out of lives against it, or for very rare instances, the Egg Dealer will sometimes hurt itself ''during its opening attack.''
-->"Behold, my latest and ''GREATEST'' creation!... N-no, wait! '''''ABORT LAAAAUNCH!!!''''' "
* Eggman saying "What?" on two occasions. In the "Black Comet" Hero ending, before the boss fight, he sounds completely dumbfounded as to why Shadow wouldn't want to give him the Chaos Emeralds. In the "Cosmic Fall" Dark ending, before the boss fight, Eggman sounds rather disproportionately aggravated, as though he resents having his little monologue interrupted.
* This exchange:
-->'''Shadow''': Not ''you'' again.
-->'''Sonic''': Nice to see you too.
* Playing as '''Maria''' is possible in the levels The Doom and Lost Impact. What makes this even funnier is that she can break down walls, robots, and other things.. [[SuperStrength just]] [[BareFistedMonk by]] ''[[ArmorPiercingSlap slapping]]'' [[BewareTheNiceOnes them]].
* In Westopolis, you can pick up a signpost and ''brain people'' with it.
* In The ARK levels, sometimes a GUN soldier will shout out, "Mr. [[CreatorCameo YujiNaka]] is alright!"
* In the Last Story, Black Doom poisons Sonic and friends with a paralyzing nerve gas. Unfortunately, Sonic and Amy react more like they've smelled something ''really'' bad.
* This gem from the Egg Breaker fight in Digital Dimension:
--> '''Espio''': (said while you are fighting Eggman after destroying one of his robots) Stop! We can't let Eggman know we're here!
* And of course, [[MemeticMutation this line]]. The emphasis on 'Damn' just makes the whole line seem insanely silly.
--> '''Shadow''': Where's that [[AvoidTheDreadedGRating DAMN]] fourth Chaos Emerald?!
** In fact the blatant overuse of 'hell' and 'damn' in a clear attempt to make the game seem DarkerAndEdgier makes the entire thing utterly ''hilarious''.