The G-Man from Half Life
We don't actually know enough about him or the ongoing plot to clearly pigeonhole him as a villain, but that is the common perception, basically because he opposes and manipulates "the Freeman".
He's basically a deus-ex-machina made flesh, or at least suit and tie, and his greatest accomplishment is to make the players self-conscious of their ignorance. Thus he is not a villain because he helps the Combine who conquered the world and kept earthlings from having sex, but because he undermines our immersion into the Freeman persona that is the whole point of Half Life's narrative.
He menaces us as gamers and not as characters, the stuttering bastard :)







