The entirety of the conversation with Weasel, should Deadpool be with you.
Weasel: Oh.... Hey Deadpool.
Deadpool: WEASEL! Old buddy..... Havn't seen you in a while. Where've ya been hiding?
Weasel: In the hospital... You broke my leg, remember?
Deadpool: Oh yeah..... But I had to. You were about to eat the last cheesy puff.
Weasel: Those were my cheesy puffs!
Deadpool: That's not how I remember it!
Deadpool's simulation mission in the original has him claiming his origin is a mixture of Storm, the Hulk, and Thor's, and then further going on to infuriate Arcade by enjoying being in Murderworld. He even mentions in the main game that the only letdown of being there was that he did not get a T-shirt (while talking to Vision in the Sanctum Sanctorum).
Deadpool arguing with the developers in the first game's credits sequence.
Deadpool: I can take down any of those goody-two-shoes wimps!
Designer: The Hulk?
Deadpool: Okay, maybe not him, bu-
Designer: The Thing?
Deadpool: Sure! If he had a cold....
Deadpool: Look Poindexter...
Deadpool's unique conversations in MUA1 especially his talk with the Ancient One.
"Stretchy man suggest Hulk release anger with words. Hulk call it 'Hulk-ku'"
"Hulk smash wide load sign;"
"Not appreciate insult;"
"Hurt Hulk's self image."
"Hulk break lots of things
"Everything make noise when broke"
"Hank wrong about mimes."
Or the best:
"Hulk want hug kitties;"
"But they so easy to squish;"
"Hulk live in cruel world."
The recording Fury left for Stark:
Computer: (Fury is trying to activate the self-destruct protocol for Prison 42) There is not enough free memory to run this program. Quit one or more programs, and try again.
Fury: Stark... your IT department sucks.
Some of the early boss battles can be this when it's 4 on 1 against a fairly easy foe. Bullseye in particular will end up getting curbstomped by four heroes in a pretty hilarious image.
An announcement comes over the PA in Stark Tower saying "Warning, a small thermonuclear device has gone missing, and Deadpool was last seen in the weapons lab". Later on, you can hear one announce that Deadpool has returned the device - it didn't make a very good basketball.
The Stark Tower PA is good for a lot of funny, from Johnny Storm leaving a prank "Happy 65th birthday, Ben Grimm" announcement to reminders that "Miss Bambi and Miss Heather" are still waiting for Tony in the main lobby.
Deadpool will make an interesting comment if you have him in your party when you go anti-registration.
Commander Maria Hill: You don't know what you're doing!
Deadpool: Par for the course, crazy lady! Besides, I can always go the other way on my next play-through.
Dr. Doom (even if beating a basic mook): *levels up* Finally! I have achieved my ultimate triumph!
During the first intro movie in MUA 1, Wolverine is seen pulling a large piece of shrapnel from his back while Thor, Captain America and Spider-Man look on.
Wolverine: What are ya girls lookin' at?
The credits of the first game has several of the characters recording their lines. They're guaranteed to make you laugh.
Xavier gets into the mind of the script writer to stop making him repeat his lines or else he'll make him relieve a very bad childhood fight.
Galactus keeps breaking things in the recording booth.
Mr. Fantastic can't pronounce 'nuclear' right.
Loki is scared that Thor came early for recording since he glued his hammer to the floor that morning.
Ninjas keep attacking Fury.
Jean hates that she always dies.
Mephisto has a lot of friends in Hollywood since he makes deals with people for their astral souls...
Spider-Man can be quite snarky in this game, and it's always hilarious.
Fury: You'll be travelling to Mephisto's Realm. It's a dimension of fire and brimstone.
Spider-Man: Why can we never go to a dimension of lonely super models?
"Am I dead? Why does heaven smell like a wet dog? (notices Wolverine) Oh. Never mind."
The endings of MAU 2, playing the Anti-SRA path, there will be a dialouge about Deadpool complaining to one of the developers that he was told that the game was suppose to be "Deadpool and his Inferior Friends". In the Pro-SRA path it'll be Hulk in a talk show.
In MAU 2, you get a special team bonus if you make a squad with Spiderman, Deadpool, Iceman, and the Human Torch. The name of the team? 'Just Shut Up, Already!'