Also, in the ending, Team Chaotix suddenly remembering they never got paid. For extra points, Eggman is trying to sneakily tiptoe away when Vector realizes this.
Vector: That slime ball!!!
Rail Canyon, with Team Sonic, with their first encounter of a bullet train.
Tails: Sonic, look out!
Sonic: WHOOOOAA!!! (first genuine loud freak out)
Similarly in Hang Castle, near the end of the level. Team Sonic falls off of a rail into what appears to be nothing, accompanied by one of the "death by fall" clips.... then you hit one of the reversing switches, and sometimes you'll get Sonic giving a hilariously timed Flat "What.".
During the Egg Hawk cutscene with Team Chaotix, this little exchange occurs.
The end of Team Sonic's story has Knuckles teasing Sonic, claiming that he couldn't have made it through the venture alone. Sonic... agrees and thanks him for the part he played. His expression is priceless.
Omega gets a pretty funny line if he pulls off a large kill combo.
*Bonus points appear*
Omega: Worthless consumer models!
This gem from Charmy during the Metal Madness fight.
Charmy: Incomplete freak!
If you leave any of the members of Team Chaotix idle for a bit, they'll usually get in a chuckle-worthy line.
Vector: Darn, I forgot to pay the electric bill for the office.
Someone discovered the unedited lines of what Team Chaotix sing during their Team Blast. The result is pricelss.