Charles' hilariously bad "mutations" pickup line. Particularly the second time around. Even funnier is that first time around it appears to be working! What makes it even more funny is that it's basically the same speech that (with Xavier narrating) opens the first X-Men movie, so it's essentially a Patrick Stewart Speech being used to pick up chicks.
When Moira finds Xavier drinking a yard of ale after he had just read his thesis on mutations.
Moira: Congratulations. Xavier: Oh, thank you. It's harder than it looks. Moira: I was referring to your thesis.
When Charles convinces the Man in Black to come with them.
Professor Charles Xavier: Would you like to see another magic trick? Man In Black Suit: Yes! Professor Charles Xavier: (Using powers, gives order) Get in the car. Man In Black Suit: Good idea.
What makes it great is that, as a PG-13 film, they had exactly one "fuck" to use before bumping up the rating to an "R". So they gave it to Wolverine.
What makes this more funny and badass is how he is smoking and drinking, in an age where these are pretty much verboten in films. And just the casual way he bitch slaps two of the most powerful mutants and their reaction is all, "Okay, we'll leave him be."
Emma Frost uses her powers to make an illusion of herself for a Russian general to have sex with while they are "negotiating". Charles and Erik burst in and see the general making love to thin air, and the two of them share a prolonged, silent "WTF?" reaction.
Havok and Banshee get a few during the training montage, with the former making Charles rush for the fire extinguisher in a panic and getting knocked over by his power, and the latter failing to fly from a window and landing in the hedge, and then getting pushed (by Erik) off the top of a satellite dish.
Doubly hilarious is the conversation just before he's pushed.
Banshee: (to Xavier) I trust you!
Xavier: I'm touched.
Banshee: (about Hank) I don't trust him.
Xavier: (to Hank) Say nothing.
Banshee: I'M GOING TO DIE!
Xavier: All right, look. We're not going to make you do anything you aren't comfor -
Erik: Here, let me help. (shove)
This bit afterwards:
Xavier: Erik! Erik: What? You know you were thinking the same.
And then later this scene comes back in an amusing way when Banshee is about to drop out of the Blackbird to locate Shaw's submarine, where he notices Erik is coming up behind him to the open bay doors. Clearly, getting pushed from a great height once by Erik was enough.
Banshee: Whoa! You back right off!
(Erik knowingly smirks and raises hands apologetically)
And from the deleted scenes, Dragneto:
Particularly Xavier's line immediately afterwards.