Deadpool getting stabbed in the ass by Morrigan's tentacles in the first intro movie of the game. Morrigan's reaction is priceless. Heck, Deadpool himself is a walking CMOF. Some of his noteworthy moments:
Change characters out for him, then don't move and watch him make a fool out of himself.
How did we go this long without mentioning his Shoryuken? Or the fact that it's a reference from his first comic series which he used to punch out Shadowcat in order to goad Wolverine into a fight? Or that the attack consists of him hopping and flailing his arm ineffectually (yet sets up the enemy for an air juggle)? Or the way he says "SHORYUKEN!!" in the way only Deadpool can? Or that the Shoryuken is referenced again in his own video game?
Character's winquotes against Deadpool tend to also be hilarious. Surprisingly funny one from Shuma Gorath:
I did not appreciate being called calamari. And what is this "dipping sauce" you keep referring to?
From the second intro movie: Amaterasu and Joe running up Super Skrull's arm, only to end up catching nothing and going Oh, Crap when they find themselves learning that Gravity Is a Harsh Mistress.
Nate Spencer and Iron Man's specific pre-match taunts:
Iron Man: Just the arm? Why? Can't afford the rest of the suit?
When she beats Deadpool to end a match, she says that if the game were made in the nineties, she would be the one hitting him with a health bar.
Also her ending, where she stars in a series called "Jen's Justice". The guests this time are Phoenix Wright and Miles Edgeworth. When Jen gives her verdict, she breaks the table. The reaction of both Phoenix and Miles is priceless.
X-23's ending, where she confronts Logan on the smoking ruin of his front lawn, in front of the Elder God she just took down, and claims the title of Number 1 since he never did anything like that. His response is basically "Yeah, yeah, now get that thing off my lawn."
Ghost Rider: "Hell hath no fury like a flaming skeleton on a motorcycle."
Taskmaster's ending. He starts a fitness program for people that want to "train with the guy who beat Galactus", and then goes on to create a bunch of exercise DVDs as well as a line of clothing named after him.
Nemesis' "time's up" loss animation? Standing still and... dropping his rocket launcher. Nothing else.
Also, one of his text win quotes is simply "." and nothing else.
While most characters' defeat quotes have then quietly muttering disappointment in themselves or the situation (with the exception of Deadpool, Rocket Raccoon will go out screaming at the top of his lungs: "I'LL KILL YOU, YOU SON OF A...!" Oh and if you beat him with a light attack:
"Promise me... no zoo."
Rocket Raccoon's win-quote against Chris Redfield.
"That's for letting them mess up Raccoon City, you wanker!"
And his victory quote for defeating Nemesis. "Man, you ugly!"
Frank West's Level 1 hyper, which begins with him jamming a Servbot head onto his opponent and only gets better from there. For added hilarity, try it on M.O.D.O.K. (enormous Servbot head) and Shuma-Gorath (one-eyed Servbot head).
One of Albert Wesker's new "Winner!" screen quotes has him bragging about how expensive his custom-made sunglasses were.
Phoenix Wright convicting a bad guy? Awesome. Phoenix Wright convicting a good guy? (eg: Captain America, Spider-Man or Thor) There's where the fun comes in accusing the good guys with something they might not have done or done so little and get huge damage as a payback.
Amaterasu is a known turnip thief, Doctor Strange is way behind on his taxes, and Iron Man should have known that hitting on Tron would come back to bite him.
Nova: "Blue blazes! I'm awesome!"
Nova: It's times like this I miss being a New Warrior. Speedball would point and laugh at you right now.
There's also "Really? I mean, really?" when he faces Viewtiful Joe.
Shuma-Gorath's ending. After defeating Galactus and being hailed as a hero, he goes native in a most hilarious manner- he becomes the host of a Japanese game show.
Shuma-Gorath: Welcome, vile fleshling scum!
The dissonance between a character's win pose and win quote can be very amusing.
Ghost Rider (after beating Phoenix Wright or She-Hulk): So I have this contract with Mephisto I'd like you to look at for me. *rides away on his motorcycle*
Doctor Strange (after beating Hsien-Ko): Your condition... my magic might be able to help. *teleports away*
Hsien-Ko (after beating Shuma-Gorath): Oh, my clothes are all slimy now! *smiles and winks*
Hsien-Ko (after beating Nemesis): Oh man, that was really frightening! *smiles and winks*
Galactus (after being defeated): How dare you! I now must squash you like the bug that you are! *falls off the stage*
A similar moment can happen if Akuma wins by time out against Thor, Amaterasu, or Shuma-Gorath. Obviously, whichever of the latter characters would still be conscious, but according to Akuma...
Akuma: I HAVE KILLED A GOD WITH MY FISTS!
One of Rocket Raccoon's win quotes brings up the inevitable response to his inclusion in the game.
Rocket Raccoon: Say how embarrassing it was to be beaten up by a raccoon one more time and I'm going to beat you up again.
The Galactus reveal trailer. After the first half with the battle against the Heralds is shown, it goes to the fight with Galactus himself. Almost immediately, Ryu jumps into the fray, delivers a Shoryuken... and Galactus flicks him away like a bug.