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.
Even funnier? Donald and Goofy are squashed against the dome of the cockpit as it falls downwards with Goofy squashing Donald even further!
The first instance of Goofy's intelligence is shown when he and Donald first arrive in Traverse Town, Goofy suggests they should start looking alleyway of the First District for the "key", but Donald dismisses this as Goofy being an idiot. Had Donald simply listened to Goofy, they would have met Sora much earlier.
Goofy: [pointing to alley] Uh, Donald. Ya know, I betcha that... Donald: Aw, what do you know, you big palooka? Goofy: What do I know?
And then everytime Sora leaves an area in the Second District, he conveniently misses Donald and Goofy, who just so happen to enter the district the minute that Sora leaves.
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]
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.
When Donald and Goofy encounter the Heartless for the first time, Donald boasts about fighting them. Cue the two getting an offscreen beating that sends them flying into the air and crashing down onto Sora.
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! Donald and Goofy almost die laughing.
During the battle with the Queen of Hearts in Wonderland, attacking her will knock her upside down to reveal her heart-patterned underwear. Even some of the Heart cards will stop to laugh at her, too. Either that or they're completely freaking out over the fact she was knocked over.
Phil's introduction to Sora and co. They enter the Coliseum and Phil, not seeing them, thinks that Hercules is there and tells Sora to move a heavy pedestal. Sora tries it, declares in his rather kiddish voice "It's way too heavy!" leaving Phil to wonder when Hercules became such a pipsqueak, until finally he turns around.
Just as in the original film, people count how many words Phil actually uses when he says he has only two. It quickly reaches Running Gag status.
After you win the Hercules Cup, Sora concludes that his strength comes from his friends. Phil is about to protest, but Herc literally picks up the satyr to affirm Sora's lesson.
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!"
When beating the Hades Cup, Hades himself is seen stood behind a gate scowling in defeat... only for Donald to hop up behind him and use a Blizzard spell to put his hair out.
After sealing the Keyhole in Deep Jungle, Terk seems to be coming on to Donald, despite being different species.
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 to make sure he's not just imagining seeing him.
After the fight with Jafar, he uses his third wish to become a genie like he does in his source material. Also like the source material, you have to go after his new lamp. Which is held by Iago. You know what you must do. And the best part is, since Kingdom Hearts: Chain of Memories and Kingdom Hearts coded retread Sora's adventures, you get to do it all over again.
After being swallowed by Monstro, you notice that Goofy is holding his shield over his head as Gummi blocks seem to rain down on him. He tells Sora to "expect showers *CLANK* heavy showers".
Also related to Monstro, there's something oddly humorous about the fact that the first fight against the Parasite Cage takes place inside the whale's bowels.
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!" In other words, Pinocchio's own nose just called him a Drama Queen!
As you progress through the 100 Acre Wood minigames, Owl shows up to explain them. When you get to the bouncing one with Tigger and Roo, he does the same... only for Roo to point out that Owl doesn't bounce like they do. Owl concedes he has a point and flies off to let Tigger explain this one.
In the aftermath of the Rabbit minigame in the Hundred-Acre Wood, Rabbit mixes carrot top juice to slim Pooh down enough to get him out of the hole in his house. Sora gets a running start to push Pooh, causing the poor bear to go flying out of the hole, right into a gathering of Rabbit's vegetables. Rabbit's utterly horrified look through the hole will definitely get a laugh out of you.
How about finding Eeyore's tail? To get further in the story, you have to send Pooh flying off of a swing. Doing it correctly has him land on Eeyore's stick house, which Rabbit was in the midst of rebuilding, where his tail somehow found itself.
Ursula's confrontation:
Donald: Come out! You can't hide! Sebastian: Yer time has come! *Ursula comes out, glaring at Donald and Sebastian*
Donald and Sebastian: AAAAAAAAAAAH!
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!!!"
The Crocodile in general is this. Contrary to real world crocs, which aren't actively hunting for humans outside of their territory, the one that took Hook's hand is actively a jerk against Hook, gleefully stalking the pirate to no end to Peter Pan's (and our) amusement.
The three's transformaions in Atlantica give us a funny detail. While Sora is a merman with a dolphin-fin, Donald is a cecaelia, Goofy is a sea turtle... with Goofy's usual head on its body, creating something that looks gloriously goofy. Pun intended.
When the Ansem-possessd Riku refers to Kairi as the last Princess of Heart, Sora goes, "Kairi's a princess!?"
The way Donald and Goofy are removed from the fight with Ansem-possessed Riku. Goofy doesn't make it into the field in time and runs straight into the barrier (complete with cartoon sound effects). Donald attempts to attack Ansem only for Ansem to casually knock him out of the battlefield like he was nothing.
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.
In the final cutscene after the credits, when Sora, Donald and Goofy are chasing after Pluto, Donald and Goofy are running to keep up with Sora. How fast is Sora running? Donald has to hold his hat on his head to stop it from falling off as he keeps up with his friend.
