What's Team Chaotix's solution to a technical problem? Smash the computer! Believe it or not, it works every time.
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.
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.. justbyslappingthem.
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. 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, this line. The emphasis on 'Damn' just makes the whole line seem insanely silly.