One line that is a bit more recent but still sends shivers down my spine is from early on in Starcraft 2 Heart of the Swarm where Raynor says "We moved heaven and earth to bring you back Sarah!" I had never heard that heaven and earth phrase before and it really stuck with me.
Also any of the comments that characters make in Starcraft 1/2 when given the move order are all stuck in my head. "Yeah I'm moving, Roger That, I read you, sir" and so forth.
Another one that I actually contemplated yesterday for way to long was a comment from GTAIV, which as a game I felt has a number of poignant and memorable quotes. I was thinking about how during the bank robbery mission, when you are having a shootout with the cops, several specific lines are spoken by Niko unique to this one instance where you have to kill police officers to proceed. The one that sticks out is when Niko exclaims (slight paraphrasing probably) "Go home to your family, you don't want to die here!" I always felt that's what made Niko an interesting character, he is a mass murderer but depending on your playstyle, he can actually be sort of sympathetic. An alternate line that is more catchy (they used it in the popular trailer) is Niko exclaiming "I'M THE ONE WHO SURVIVED" when confronting that spoilery guy.
"Get over here" is one that I always get confused over because I have personally never played the MK games, I suck at fighting games and I only prefer the spectacle of them so I just watch clips and read about them. Since I never played the original games I am always confused over which is the true line that Scorpion says, "Get over here" or "Come here." Does he say both alternately, is one used in like MK2 or something.
Also, I heard an audioclip from a really fan sprite animation where it sounds like Scorpion's voice actor had a line where he said "Get the fuck over here." Was that ever in a game or was it just someone imitating the voice?