Axel trying and epically failing to give inspirational speeches. It gets to the point where Xion actually cuts him off with, "Yeah, we got your hokey speech memorized, Axel."
When Axel informs Roxas of what he intends to do for his vacation day.
You can equip joke weapons for all of the playable Organization XIII members. All of them are quite amusing, but the most hilarious one is Saïx's, which is a GIANT. BANANA. His Limit Break can also be hilarious. Instead of mashing A, hold it down.
"Roxas, that's a stick."
One of the recon points in the Beast's Castle with Xaldin:
Roxas: Nice sofa.
Xaldin: No breaks, Roxas.
Lexaeus taking Roxas into the tutorial on how to use Limit Breaks and literally punching Roxas into critical health so the player can practice. His matter-of-fact dialogue is what makes it; the gameplay models somehow manage to make it funnier.
Lexaeus: [A Limit Break] is the most powerful move at your disposal - one that only works when you are on your last legs.
"Do you always have to stare at me like I just drowned your goldfish?" Magnificent Bastard indeed.
The Organization is having a meeting discussing why Xion went rogue. Saix mentions that no one ever reported such a thing happening before, and Axel gets an uncomfortable look on his face. Saix clearly wants to say, "Axel, is there something you neglected to tell us about?" Unlike most moments, this one is funny on account of being awkward.
Said scene also contains one of the best instances of Voice Grunting in the game: the scene opens up with everyone sitting in Where Nothing Gathers, with the world's usual somber background music playing... and then the silence is broken by a Big "WHAT?!" from Demyx.
The entire cutscene when Roxas asks Axel what love is.
Roxas and Xion feel a bit awkward, internally, about keeping their identities a secret to the Genie.
On the 11th day, Saïx tells Roxas that he'll be working with Larxene today. Roxas says "Right. Larxene. Umm..." and looks around the room for her. No-one's there, except for them two and Xigbar... who looks up and gives off an "Is this about me?" look.
Larxene telling Roxas to leave her alone and literally suggesting that he goes and hits his head against the wall.
A lot of Larxene's lines, really, especially "...Oh, dream on. It's never gonna happen" in response to Roxas staring at her.
The very, very first thing Larxene ever says to Roxas if you approach her on Day 7 (the first playable day) in The Grey Area is "Eww. You're awake?"
Your reward for defeating the Ruler of the Sky? Its dead body crashes into Captain Hook's ship!
"The only thing you could ever save me from is boredom."
From the 1.5 remix: Roxas scaring Axel on the clock tower.
In Roxas's journal, he notes that Axel told him that the ice cream was the "icing on the cake", but there was no cake, only the ice cream.
This one is really only amusing if you play Ace Attorney, but when investigating The Usual Spot (called Under the Tracks in Days) in Mission 23 (when searching for the missing Xion), you can examine the stepladder in the corner, which Roxas (somewhat surprisingly) refers to accordingly as a stepladder.
This line when talking Organization XIII's moogle shopkeeper on Day 51...
Moogle: I heard you collapsed, kupo. Gotta pace yourself, kupo. Who else am I going to swindl—talk to, kupo?
When about half the members head off to Castle Oblivion Luxord whines that half his poker league is absent. The thought of the entire Organization regularly sitting down to play poker is kind if hilarious.
On a similar vein there's something rather funny about the mental image of Axel, Roxas and Xion standing in line to buy ice-cream, black cloaks and all.
Followed by Demyx's attempts to weasel their way out of having to take Phil's training, first by challenging Phil to a wrestling match under the assumption he'll be fighting Phil, increasing his chances by secretly taking a bottle of steroids. Then Phil reveals that Demyx will actually be taking on Hercules, causing Demyx to freak out a bit. So when he and Hercules are about to start, Demyx blinds Hercules and Phil with his water (shooting water balls in a Spider-Man manner) before attempting to strike Hercules from behind, only to break his entire hand! Needless to say, the whole experience was pretty much an affirmation as to why Roxas and Demyx should partake in Phil's training.
The discussion of Roxas having "pushed the wrong buttons" with Xion. In the manga, he discusses it with Demyx just as he's coming out of the shower. Demyx wonders to himself if they're good enough friends to talk with each other about stuff like that, and then gives Larxene as an example of a girl who was covered with wrong buttons because everything he said to her seemed to be wrong. He would apologize to her, not knowing exactly what for, only to be told by her not to apologize if he didn't know what he was apologizing for. Later, Roxas writes a letter to Xion that says "Sorry for pushing your buttons," complete with pictures of buttons that look like the ones on a PlayStation controller. And then there's Axel's look when he shows the letter to him.
On the first vacation day, the reader is treated to a page showing off how the other Organization members are spending their time. Many are doing predictable activities (i.e. Demyx is playing his sitar, Luxord is playing solitaire), but Xaldin is getting his hair done by a Dusk while Xemnas is just staring at Kingdom Hearts dramatically.
After helping Xion escape, Riku is ambushed by six members of the Organization, and winds up surrounded. How does he escape? He tricks four of them into attacking each other.
First, when Xigbar tries shooting Riku, Riku simply ducks, causing Xigar's arrow-bolts to hit Demyx.
A bewildered Demyx angrily attacks Xigbar with a burst of water, only to accidentally hit Xaldin instead.
Xaldin, drenched and sputtering, summons his lances, all with a Hidden Eyes expression.
The way Luxord is provoked has to be the crowning moment here.
Luxord: According to the cards— (cards are cut by Xaldin's lance, prompting Luxord to suddenly don an ominous glare along with a cross-popping vein on his right temple) Oh, it's on!
Xion's reaction to Pluto tackling her out of nowhere is simply freaking adorable!
Roxas visits the ice cream shop, only for Riku to appear. Roxas tries to attack him, but Riku stops him, saying that they're in public and shouldn't fight, less cause a lot of attention, or worse, get innocent people wounded or killed. Then the shop owner, an elderly woman, sees them bickering.
Woman: Oh, my, my. You mustn't fight.
Riku: Oh we weren't. It's just that I offered to pay, and he didn't want to let me.
A cardboard box reading The Oranges That Never Were
The start of chapter 26 has Saïx wondering why his computer isn't logged off. Then it is shown that Demyx hacked it to copy the reports of others. There's a mood whiplash as Xion was the next one to use it to search for Castle Oblivion. Then Xaldin was the next one shown trying to use the computer, threatening to smash it if it doesn't show the weather reports.
Saïx taking out his frustrations against Demyx for hacking his computer by sending him and Roxas to train in the Colosseum. Demyx digs himself deeper when he mentions the poem Saïx has in his computer, causing Saïx to enter his Berserk Mode and demolish him.
The Organization's winter break (without permission). Several members decide to take a day off due to a strong cold wave that hit The World That Never Was, with Saïx caving in soon after. Though they decided to work anyway due to a bad smell that they blamed on Vexen. It actually came from some soybeans that Zexion was fermenting with the table heater.
Axel being called a nanny by Xigbar, Xaldin, Luxord, and Marluxia. And him sitting down on a whoopie cushion with Larxene and Demyx laughing in the background.