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 life under the belief that you are a six-year-old girl. Logan: Would you really do that? Xavier: I'll have Jean braid your hair.
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.
Bobby introducing Wolverine to his alarmed parents as "Professor Logan". His mother asks him as he's leaning against a doorway in an undershirt what he teaches and he deadpans: "Art."
More of a heartwarming example, but when Nightcrawler explains his markings 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 righ tin the face of... the family's pet cat. Who is completely unperturbed and starts licking at one of them.
As a Call Back from the first movie, Wolverine moves from stealing Cyclops' bike, to his car. Lampshaded by Pyro.
When Bobby is freezing his mom's tea cup, this exchange follows.
Mrs. Drake: This is all my fault.
Pyro: Actually they discovered the Mutant Gene is carried by the males, so actually it's his (Mr. Drake) Fault.