- Sonic telling Emerl to ignore Knuckles. This is pulled at a time when he has just barely realised how Emerl works, meaning Emerl genuinely ignores Knuckles. Sonic is Trolling Knuckles.
- The end of Cream's chapter, where Sonic compliments a frozen, angry Eggman on "his new dance."
- Also in Cream's chapter, while Emerl and Cream are training in preparation for a fight against Chaos Gamma, Eggman tries to call them on the computer nearby. Neither of them pick up, which leads to Sonic not believing that Eggman has anybody hostage.
- The name of Skill #003, Sonic's Air Action: "Sonic Ballet". Tell me that doesn't conjure up funny mental images.
- During Tails' playthrough, you can actually forfeit the fight between Tails with Emerl and Rouge (through the pause screen). It plays out with Tails losing and having to do what Rouge wanted. Rouge gives him the pass anyway, but not before she gives him a kiss on the cheek. Tails' reaction as well as the fact Rouge was doing this just because she liked to tease Tails is pretty funny.
- After Emerl spilled out his guts, Shadow complained that there's no reason for a weapon to have feelings and left. Sonic replied that Shadow could be learning something and be more honest about himself (The fact that Shadow viewed himself as a weapon at that time yet does have feelings as well). It was the way Shadow said it that was funny.
Shadow: Hmph... There's no reason for a weapon to have feelings! This is ridiculous! I'm leaving!
- Eggman tries to lure Knuckles and Emerl to his base Gimme Shelter. How? By shouting "THEY'LL NEVER FIND MY HIDEOUT AT GIMME SHELTER, LOCATED IN NIGHT BABYLON!" When this works, he says that he deserves an award for his acting.