The best one is from God of War 3. If you've played it to the end, you'll know the inflection:
"GAIA?! YOU. LIVE?!"
Also, in MGS4, when Otacon's explaining shit in the helicopter as they fly out of South America at the end of Chapter 2, and Raiden's all weak on the helicopter floor, and Snake pops out of the corner crouching and goes, "Whaddaya mean?"
Always cracked me up. I picture him popping up to say that everytime someone's confused.
Also, I wish I could quote Nigel West Dickens from Read Dead Redemption. Anything he says, really -- it's all gold.