My current favorite quotes have to be from Deadpool in X-Men Legends 2 and Marvel Ultimate Alliance when he levels up :
X-Men Legends 2
"I win! I win! Neener Neener Neener!"
Marvel Ultimate Alliance
"And now I'm better, at doing whatever it is Wolverine does"
"Oh! Did I win a new car too?"
Of course he has random quotes during M:UV as well :
(Flirting with Black Widow in a bad French accent)
Ah, how I have missed you, mon petit chapeau. Let us run away and live a carefree life somewhere exotic... like Pittsburg.
[separate Black Widow conversation]
Deadpool: Black Widow, I've gotta know... Are those real?
Black Widow: I beg your pardon?
Deadpool: Ahh... Your teeth, they're just so darn shiny and straight.
(Talking to Jarvis)
Hello, good citizen! I'm CAPTAIN AMERICA! You don't have to salute if you don't want to.
(Jarvis doesn't believe him)
All righty then, I'm THOR! You might want to kneel in my presence... I am the God of Thunder, you know!
(Talking with his buddy Weasel)
Deadpool: Weasel old buddy! Where have you been hiding out?
Weasel: In the hospital, you stabbed me in the leg remember?
Deadpool: I had to! You were trying to eat the last cheesy puff!
Weasel: It was MY bag of cheesy puffs!
Deadpool: That's not how I remember it.
(Talking to Black Bolt)
Deadpool: Hi, Black Bolt. How are ya?
[Black Bolt says nothing]
Deadpool: Oh, that's right. You can't talk can you? Your voice is so powerful, it would destroy half of Atillan if you said anything at all.
[Black Bolt still says nothing]
Deadpool: But c'mon, let's put that to the test. Just say one tiny word: 'Spatula.'
[Black Bolt still says nothing]
Deadpool: Oh, don't be such a stick in the mud. Come on, repeat after me: 'Spatula.'
Sorry for the long post, he just has too many funny things for me to list without making this a giant wall o text