Professor X dissuades Wolverine from smoking in Cerebro.
Xavier: Logan, my tolerance for your smoking in the mansion notwithstanding, continue smoking that in here, and you'll spend the rest of your days under the belief that you are a six-year-old girl. Logan: Would you really do that? Xavier: I'd have Jean braid your hair. Welcome back.
Even better, Wolverine puts out his cigar by pressing it in the palm of his hand (after he looks around for something suitable to use as an ashtray). Thanks to his healing factor, all he does is wince slightly.
Whenever Nightcrawler tries to introduces himself ("My name is Kurt Wagner, but in the Munich circus I was known as the Incredible Nightcrawler"), he's interrupted.
The whole scene of Logan and Bobby in the X-Mansion kitchen late at night. They make a surprisingly good comedy duo.
Logan finally finds a bottle of soda in a cabinet, but it's warm. Without saying a word, he hands it to Bobby who blows on it to instantly chill it.
Logan: Thanks.
Bobby: No problem.
When Stryker's soldiers are carrying a tranquilized Siryn out of her room, they're stopped by a steeled-up Colossus standing in the doorway. One of them tries shooting him, and he just gives the briefest glance down, as if silently asking "What did you actually think that was going to do?" Cut to the unconscious soldiers crashing through the wall.
Bobby introducing Wolverine to his alarmed parents as "Professor Logan". Mr. Drake asks him as he's leaning against a doorway in an undershirt what he teaches and he deadpans: "Art." Pyro visibly has to stop himself from sniggering, while Bobby's brother is not amused.
While hiding out at Bobby's parents house, he brings Rogue some new clothes and turns around while she changes in his room...but not before getting a little sneak peek.
More of a heartwarming example, but when Nightcrawler explains the markings on his skin it becomes quite humorous.
Storm: How many?
Nightcrawler: One for every sin. So quite a few.
A tense moment in the jet is interrupted by Magneto and Mystique laughing like the popular girls in a high school movie. "We love what you've done with your hair." At that, Rogue takes a glove off and needs to be held back.
At Bobby's house, Wolverine is drinking some beer, when he hears something approaching. He turns and lets his claws out, sticking them right in the face of... the family's pet cat. Who is completely unperturbed and starts licking at one of them.
You can also hear the cat yelp when he retracts them in surprise when the Drakes return.
Adding to the humor, he doesn't retract them right away, letting the cat check them out with a bemused look on his face.
The novelization adds another fun bit in how, for the first time, Logan realizes what people feel like when they see him pop his claws.
When Mystique has snuck into Stryker's lair and is fighting guards, she escapes by sliding under a door while giving Stryker the finger.
And then, when she's gotten to the control room by disguising herself as Stryker, and seals herself in just as Stryker arrives, she blows him a kiss and gives him a wave just before the doors shut, while still using his form.
Both become even funnier when you watch X-Men: Days of Future Past and find out that Stryker's got kind of a track record of being tricked and beaten up by Mystique, possibly explaining why he immediately ordered her to be shot when he realised who "Wolverine" actually was.
On the trip from the school to Boston in a Cyclops' car, they reveal their dislike of boybands:
Pyro: I don't like uncomfortable silences.
Rogue: What are you doing?
Pyro turns on the radio; N Sync's "Bye Bye Bye" blasts out.
Lady Deathstrike's first attempt at knocking Cyclops out. She strides into the room and casually shoots at him with a dart gun... which does nothing because Cyclops is wearing body armour. He just stares at it for a second before blasting her into the wall like this happens to him all the time.
When Wolverine returns to the mansion at the start of the film:
Wolverine: Who's this guy?
Rogue: This is Bobby, he's my...
Bobby: I'm her boyfriend. (shakes Logan's hand and freezes it) Call me Iceman.
Wolverine: Boyfriend? So how do you guys...?
Bobby: Well, we're still working on that.
When Magneto breaks out of jail:
Mitchell Laurio: Have a nice sleep, Lensherr?
Magneto: There's something different about you today, Mr. Laurio.
Mitchell Laurio: Yeah, I *was* having a good day.
Magneto:(gets up) No, it's something else...
Mitchell Laurio: Sit down.
Magneto: No.
Mitchell Laurio:(draws his club) I said, sit your ass down! (He starts for Magneto, who holds up his hand. Laurio stops forcibly and gasps) What are you doing?
Magneto: Ah, there it is... (he lifts his hand, and Laurio lifts into the air) Too much iron in your blood! (he draws a cloud of iron particles out through Laurio's skin, and squeezes them into a set of ball bearings. Laurio collapses to the floor, unmoving) Mr. Laurio, never trust a beautiful woman, especially one who's interested in you.
It's easy to miss, but Magneto also winks at Laurio at that line.
After Pyro destroys all the police cars and injures the cops, Wolverine gets up after being shot in the head, surveys the destruction and then looks back at Pyro. The kid smiles slightly in response. And straight after that, Wolverine gives the cop that shot him an annoyed look as the guy looks on in amazement and shock.
Mystique, having infiltrated Alkali Lake and let the other mutants in, reveals that she's found where Stryker's version of Cerebro is located due to a large portion of the dam's energy being directed to that area. Storm asks her if she can shut it down from the control room they're currently all in, to which Mystique replies "No," staring into the camera in quiet exasperation. The DVD commentary further reveals that this moment was included to shut up any nit-pickers by making it very clear that no, the characters can't just turn the Cerebro-copy off.
Magneto casually walks into Dark Cerebro and then when he meets Jason, he smirks and taps his helmet as if to say "nice try".
While it's a horrible way to die, the way Yuriko's adamantium-filled head makes a small "clunk" when she hits the bottom of the water tank earns some chuckles.
When one of Stryker's men just shoots a tranquilizer dart at Siren to shut up her sonic screaming.
Behind the Scenes
According to Hugh Jackman, during one of the takes of the Weapon X flashback where Wolverine breaks out of the tank and escapes the facility naked, he was suddenly surrounded by all the female cast members plus James Marsden's mother, hooting and waving dollar bills.
During filming, Hugh Jackman's sister visited the set. As a joke, she was made-up in Jackman's full Wolverine costume and make-up, and walked around the set. Apparently, she was very convincing as Jackman. Bryan Singer was not aware that it was not Jackman in the Wolverine costume, and commented of her work during shooting that, "Hugh is acting very strangely today."
