For me, it would be GLaDOS.
Portal 2 spoiler
She deleted the one remaining human part of herself because it was just too much to deal with. She releases you at the end of Portal 2 as a path of least resistance measure because “killing you is hard.”
What about you, what is your favorite media villain?
I would not have thought of Omar as a villain. The man even takes a stand against criminals killing people not in the game.
I bet the dealers he steals from would consider him a villain.