Hades: "Do you have any idea who you're talking to!? I'm the Lord of the Dead!" Auron: "Hhmph…No wonder no one wants to die." Hades: "You are FIRED!"
In Kingdom Hearts II, when you encounter Xigbar in The Land of Dragons, he seems to try and make a mysterious exit, by disappearing whilst Sora and co. are distracted by Nobodies. In the next shot however, you see Xigbar running off in a rather amusing fashion. So much for a mysterious exit…
Almost everything about Demyx would qualify. From "Run! Run away!" to his over-the-top death scream.
The Big Bad has just been beaten, and everyone is getting ready to go home. Sora tells Riku he's coming along too. Riku is still guilt ridden (he was the guy who caused that home to be destroyed in the first game) and asks "How am I supposed to face everyone?" Sora replies "like this", and makes a funny face that cracks him up. Remember, this is ten seconds after they beat the Big Bad, and ten seconds before he comes back as a One-Winged Angel. But they've got time to crack jokes. Thank you Sora, for reminding us this is a Disney game.
And that was a Call Back to an earlier scene in the game, in which Donald and Goofy answered the same way Sora did, when Aladdin asked what do friends do.
Earlier: "...And then, we can go see Santa! *cue Sora's dreamy pose and disapproving stare from Donald* Erm… but first, the Heartless!". It's way funnier.
And upon being shown the door to Christmas Town, Sora leans his head closer to the door with a "Whoa..." look on his face, as his friends look on in confusion. A few seconds later, the camera leans closer and closer to Sora's face, as he gets more and more exited, and then...
Sora: Come on, just open it!
Once the trio are in Christmas Town, they land, one by one, on top of each other (a running gag in the series). Sora knocks his friends off his back and looks at Christmas Town with awe. Donald then joins him, while Goofy simply lies there unconscious.
When Tifa is looking for Cloud and asks Sora if he's seen him:
Tifa: "I'm looking for a guy with spiky hair" Sora: *wordlessly tugs at one of his own spiky locks* Tifa: *chuckles* "Spikier."
Oh, you missed the best part! After that, Tifa starts looking around the room, tapping walls, opening drawers, etc. Then she turns to a wall, and SLAMS her fist into it, hard enough for the screen to shake, and dust falls from the roof. She turns back to Sora & co., grins and says "Sorry to bother you." The gang snaps to a nearly flawless attention (army style) and says "No bother, ma'am!" They wait to be sure she's gone before anything else happens.
King Mickey getting confused when Goofy mentions a password for the DTD in Hollow Bastion:
Sora and co: *looks shocked*
Mickey: "Oh! I guess you mean like a code!"
Ha! Mickey is a computer illiterate! Who knew?
Of course he is. He's what? 80? Old people don't understand technology.
The scene makes more sense in the Japanese version. They used the English word "password" which left Mickey confused for a while, until he realized they weren't speaking Japanese.
A little known part of Anti-Form can be seen here.
The blink-and-you’ll-miss-it "Like an Old Married Couple moment" between Leon and Aerith in the second game during the crisis at Hollow Bastion, when Leon, having to go retrieve the anti-virus for the computer, asks Aerith if she'll be OK on her own, and she shuts him up with nothing but a Death Glare.
In the second game, Sora, Donald, and Goofy's reaction when Mickey tells them that the "Ansem" they worked so hard to beat wasn't REALLY Ansem.
Pretty much anything involving Past Pete...
Past Pete: Say... anybody seen any bad guys around here?
(Sora, Donald, and Goofy all silently point to Past Pete)
(sound of clashing cymbals)
Past Pete: I finally found the runt what stole my boat!
Past Pete: Wait! Wait! It wasn't ME! It was some guy that LOOKS like me!
Sora getting smacked in the head with a random (flying) honey pot right after watching Pooh forget about everyone. It came out of nowhere (literally), yet you'd expect something like that to happen in the 100 Acre Wood portion.
From the second game: Sora and Donald's reactions to finding out that Mulan is a girl.
From the second game: Hades flicking Sora over to fall on the ground.
Genie's first appearance in KH2, when he flies into the palace courtyard and jubilantly hugs Pete, mistaking him for Aladdin. At one point he asks, "Did you put on weight, Al?"
"It's the guy who's NOT Ansem!"
While Ariel is distracted with thoughts of the human world, Donald offers to take her place in the musical.
Sora trying to use a computer: "Whoa... it's doing something!"
Captain Jack Sparrow. Not only one of the most popular characters in the series, but also one of most funny. Most of his lines would really make a player crack up into laughter
Jack Sparrow: I don't know who these Organizers are, but I will say they're makin' we pirates look like proper gents!
Continuing from the first game is Sora, Donald and Goofy ending up on top of each other. The first time this happens is when they were telling Auron their names. As both of his friends jump onto his back as they say their name, Sora could not handle their weight and collapses. Of course, they were cursed at the time, and he was able to pick them both up without any trouble just two worlds earlier.
This happens again in Agrabah, when they tried to stop Abu. We don't see the crash, though...
And in the manga, this happens again when they crash-landed on Sark. It also counts as a Mood Whiplash, as he was torturingTron when he got crushed.
Cid calling Merlin an old loom. Cue the wizard casting a Fire spell at the computer in anger, causing it to explode.
Stitch greeting Sora by licking him in the face whenever summoned. Whenever this happens, Sora will be teleported to a beach, so the scene is twice as funny if Sora's wearingarmor or vampire garb.
Pete and the Merchant fighting over Jafar's lamp. Pure comedy
Pete: Thank you!
Merchant: It's mine!
Pete: Lamp hog!
Merchant: Go away! *gets lamp stolen* No fair!
Pete: Heha, I win! *Iago steals lamp; Pete does not realize until he checks his hand, and has a complete freak-out.*
When the gang prepares to face off against Barbosa one last time in Port Royal, he's at first shocked to see them all alive and says it's not possible for them to have survived. So Donald steals Jack's line from the film.
While the manga adaptation has a lot of funny scenes, Kairi pulling an akanbe on Axel when she escapes with Pluto is absolutely hilarious, especially when you compare the scene with what she did in the game.
Another manga example: Sora summons Jafar out of his lamp after the party finds themselves trapped in the Cave of Wonders (thanks to Pete's greed). Jafar reluctantly grants the teenager's wish for the party to escape... and is then instantly called back into his lamp, much to his surprise and horror.
Just the way that Sora casually with the dullest tone imaginable for such an upbeat character informs Ursula after he and his friends right before Eric finishes her off that she's finished.
Sora: (in flat out, dull voice as he's diving back into the water after smacking Triton's trident out of her hands) It's over Ursula
Donald Duck grabbing Cogsworth and playing with him after the trio meet the servants deserves a chuckle or two.
This scene is mostly terrifying, but the way Sora calls Sark a "Heartless Commander" is quite funny, especially if you look at his snarky face when he says that line out.