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.
Sonic's interactions with the serious and moody Shadow deserves some mention. Here are some particular scenes:
In the scene before the Black Bull boss battle, Sonic jumps with excitement about fighting against Black Bull while Shadow just glances at Sonic in an annoyed manner and then turns to the Black Bull:
There's also the scene where the two meet each other again, and Shadow shows that he isn't very happy about it:
What's even better is that the subtitles are rendered thus: "Where's that damn FOURTH Chaos Emerald?" due to the game's weird thing about allcapsing numbers related to the Chaos Emeralds.
In fact the blatant overuse of 'hell' and 'damn' in a clear attempt to make the game seem Darker and Edgier makes the entire thing utterly hilarious.
When Shadow decides that he's going to smash open a box and just grab the Chaos Emerald powering it, first you're like "Shadow, you're a dick." Then the alarm starts blaring and the Oh, Crap look on his face is priceless. It's like "Oh yeah, I forgot about that part..." Then he has a flashback which takes him to one of the most horrible levels in the game, which serves him right.
Not to mention how amused Shadow sounds when he discovers the emerald.
Shadow: A Chaos Emerald? You've got to be kidding me, guys! This is like taking candy from a baby, which is fine by me.
It gets even funnier when you realize that the Chaos Emerald is likely powering the shuttle that Shadow is on. You know, the same shuttle heading to the Black Comet. And this can be on the path to the Pure Hero Ending.
After the Death Ruins' "Hero" level, the following cutscene is pretty hilarious. Shadow mocks Black Doom, who says that Shadow must rest for "tomorrow's ritual"...right before summoning a ridiculously big Black Bull for the hedgehog to fight.
Knuckles chasing Eggman at the end after the latter tries to steal the Chaos Emeralds!
Eggman: How about giving me those Chaos Emeralds now? (Runs off) Knuckles: Hey! Get back here, you creep! (chases him)