The scene in the sushi restaurant, and the TV interview with the "witnesses".
Horrified Monster: Well, the kid flew right over me and blasted a car with its laser vision.
"It is my professional opinion that now is the time to PANIC!"
"Oh, hey. We're rehearsing a - a scene for the upcoming company play called uh, Put That Thing Back Where It Came From Or So Help Me. It's a musical." (for added hilarity, during the credits a musical with that name is enacted...)
Mike: Put that thing back where it came from or so help me, so help me, and cut!
In the bloopers:
Mike: Put that thing back where it came from or I'll poke myself in the eye!
Later, after Boo is missing:
Mike: What are you worried about?? She's out of our hair!! Randall: What are you two doing?! Random Employee: They're rehearsing a play! Mike: (singing) SHE'S OUT OF OUR HAIR!!
The scene in the locker room where Sulley just walks away, not even realizing that Boo is hanging onto his back until he goes around a corner and then runs away screaming. And just to make it even more funny, part of the Psycho theme is playing.
Sulley placing Boo in her room, he closes the door, turns around...and Boo's right in front of him! Becomes even funnier when he glances at her door in confusion and then at her.
Also during the bloopers, the slow-mo scene where all the monsters trip and bowl over each other.
During the international/interdimensional door chase, Mike and Sulley end up in a tropical paradise.
Mike: Why couldn't we get banished here!?
Mike trying to apologize about not wanting to help rescue Boo, while an invisible Randall is beating Sully up.
Sulley:(while trying to make Boo stop crying) 'Oh, he's a happy bear, and he's not crying, and neither should you, or we'll be in trouble, 'cause they're gonna find us. So please stop crying.
"It's 'Bring An Obscure Relative To Work' Day!"
The scene immediately after the restaurant chaos when Sully and Mike are trying to deal with Boo in their apartment. For Sully and Mike, it's like they've got a wild, lethal snake in the place. For Boo, it's basically the best game of peek-a-boo ever.
Sulley and Mike banter with each other throughout the credits song "If I Didn't Have You", and it's all very funny, but this bit takes the cake:
Sulley: Yes, I wouldn't have nothing if I didn't have you
Mike: I know what you mean, Sulley! Because-
Sulley: I wouldn't know where to go
Mike: Me too! Because I-
Sulley: Wouldn't know what to do
Mike: Why do you keep singing my part?
Also, when it sounds like they're dancing.
Mike: Don't you dare dip me! Don't you dare dip me! Ow, I should have stretched.