"Ugh!" - Minecraft Man.
"Battle Routine, Set!" - Lan Hikari, Megaman Battle Network series
"Execute!" - Megaman, A.K.A. Megaman.exe, A.K.A. HUB, Megaman Battle Network Series
"Isn't there some sort of decency rule against this?" -Civilian, AC: Brotherhood
"QUICK JESUS, SAVE ME!!!" - Civilian in AC: B when you start a fight with guards or kill someone. (Quick Jesus, the speedier form of regular Jesus!)
"Wort Wort Wort!" -Elites, Halo: Combat Evolved
Anything from the RvB Easter Egg in Halo 3:
http://www.youtube.com/watch?v=B5Bt5zmJK0I
Cave Johnson's Combustable Lemons rant, Portal 2
"Do a Barrel Roll!" - StarFox 64 (surprised this one hasn't been mentioned yet)
"I hate that frog!" - Wolf O'Donnel, StarFox Command (As a direct response to the above quote)
"Tank beats EVERYTHING!" -Random Marine, Halo 3
"Were it so easy..." -The Arbiter, Halo 3
And in my opinion currently the most famous two quotes of the decade...
"Halo. It's finished." -Cortana, Halo: Combat Evolved
"No. I think it's just getting started." - Sierra - 117, Master Cheif Petty Officer John - 117
Halo: Combat Evolved