Strong Pokemon. Weak Pokemon. These are the beliefs of cruel Trainers who mistreat their Pokemon.-- Elite Four Karen, Pokemon GS Series (I may have misquoted this quote, though)

Snake *motioning to Zelda and Shiek*: Stay here! *leaves*
*Zelda waits a bit, transforms into Shiek, and she and Peach depart, giggling as they go*-- Super Smash Bros. Brawl (The Subspace Emissary, AKA Adventure Mode)

"Spoony Bard!"

"You're a little shaky."

Sam and Max Hit the Road http://youtube.com/watch?v=4yWnnk9fyJE&feature=related

Anachronox http://youtube.com/watch?v=U-yL4hrMFzI

Those two games are positively brimming with them.

 You bet kid !

*Tkschss* "Aahhh..That's the stuff" - Marine

"Metal Gear?!" - Solid Snake (David Hayter)

"POwwwWA GUYSERRR!!!" - Terry Bogard

I love so many games for its dialogue, Final Fantasies have always had nice dialogue...hmm, I love this line from Ratchet and Clank: TOD

Cronk: "Now to show my superior online capabilities!"
Zephyr: "Too bad your processor chip has a 43% failure rate, haha". Gotta love Insomniac for that one.

Oh, remembered one:

Freelancer:

Trent: "Sidewinder Fang"
Barkeep: "All We've got is liberty ale"

Why thats because a running gag between me and my friend I dont know, but it was hilarious at the time.

Portal - 'touching the floor here will result in an unsatisfactory mark on your record, followed by death'

"Remember, 'bring your daughter to work'-day is the perfect time to have her tested!"

"But there's no sense crying over every mistake, you just keep on trying 'till you run out of cake"

Actually, the entire game is one long awesome quote.