Axel trying and epically failing to give inspirational speeches in 358/2 Days. 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.
In Kingdom Hearts: 358/2 Days, you can equip joke weapons for all of the playable Organization XII members. All of them are quite amusing, but the most hilarious one is Saix'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."
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.
"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.
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, Saix 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.