Just as in the original film, people count how many words Phil uses when he says he has only two, to Running Gag status.
In Traverse Town, Sora gets exposition from Leon and Yuffie, while Donald and Goofy get exposition from Aerith. They're in the same inn in adjacent rooms connected by a door. When the Heartless attack, Sora and Yuffie rush out into Aerith's room...causing Donald to become Squashed Flat when the door slams him.
Donald tells a depressed Sora to be happy if he wants them to join him in finding Mickey shortly after they all meet. In an awkward genre-blending moment, Sora then struggles to work up a pretty pathetic excuse of a smile!
Goofy: That's one funny face!
His face is even sillier in the manga adaptation.
Donald Duck hilariously pulls off the only instance of Breaking the Fourth Wall, during the scene in which he and Goofy talk to Aerith. Donald is too short to be in proper focus of the camera, so he reaches out and pulls the camera downwards so that he can be in focus.
A subtler but similar gag has Goofy messing up his words—out of focus of the camera, Donald pokes his finger up as he corrects him.
Most scenes featuring Hades would definitely count. James Woods is in top form.
"Yo, hey, how're you doin' everybody yeah. Got a minute? Hades, Lord of the Dead. Nice to see you. Hey guess what? I got a place for you down under!"
The part where Donald and Goofy go into the Gummi Ship. First the fact that they get picked up and put into the ship upside down with Donald looking quite annoyed. Then when they are preparing to launch, a hall with a Mickey Mouse head shaped door opens up, Donald yells to blast off...then you see an arrow pointing down inside the hole and they, rather than go forward, fall down. As they fall, you hear both Donald and Goofy's signature screams.
What makes this scene even more funny is that Donald's wizard's hat seems to be glued to his head as it doesn't fall off when he is turned upside down... either that, or he's using magic to keep it on.
In the fight against Leon, he's usually too powerful to beat, and thus he knocks you out. But if you do manage to fight him off, you instead manage to bring him to his knees...and faint in the process.
Sora: [gasping for breath] N-, now...you're...gonna...you're gonna...[faints]
It's kind of a stealthy sort of moment, but the fact that Leon gives you the first summon gem in the entire franchise yet has no idea how to use it will make anybody familiar with his source game chuckle if not laugh outright.
Sora's first impulse the first time you run into Riku is to pull his cheeks.
After defeating the Ice Titan in Olympus Coliseum, the big guy does some dramatic roaring... then the camera zooms out to show that he's shrunken down to Sora's foot. Sora tries to stomp him, only for the Ice "Titan" to scurry away comically.
When you find Pinocchio in Monstro, Jiminy runs up to him all worried-like. Pinocchio opens his eyes like he's on the verge of Heartless or something and says "Jiminy... I'm not gonna make it..." AND HIS NOSE GROWS AN INCH OR SO. "Oh! I guess I'm okay!"
You can have a lot of fun tormenting Captain Hook. You can not only light his pants on fire (causing him to run around in mid-air), but trick him (or knock him off) into jumping off the ship. Bonus points if you light him on fire and throw him off the ship, causing him to run around shouting "YOU'LL NOT GET ME OTHER HAND!!!"