Richard B. Riddick.
I just saw Pitch Black, and there is no way I'd want to be anywhere near Riddick at any point in my life, ever. He's like an Alien and Sam Fisher rolled into one.
Seriously, you could put every single video game villain ever made into one game, then Riddick would come along, and get ticked that he couldn't find his cigarettes. He'd then start shooting out lights, then stalk and kill everyone else. He'd kill a person just for making him wait in line for the toilet.
Part of what makes him so scary is that he's more realistic of a character. You couldn't very well imagine Sephiroth in real life (not that fangirls haven't tried), but Riddick is bone-chilling because I can easily picture real life versions of him existing. His ability is almost irrelevant when held up next to his complete disregard for life and willingness to do anything to anybody.