I'd like to put forward the reapers, borg and zombies
they don't just kill you, they kill you and use you to make more of themselves
You left out the Cybermen from Doctor Who, they were basically the Borg before the Borg were invented. (although the Borg are cooler IMO)
Finding out Wesker is a Traitor in the first Resident Evil. (Actually Wesker is a prick in most of the games)
Being nailed by a blue/red/green shell right before the finish line while in 1st place by either my best fiend, a girl I am dating, or any other friend in Mario Kart.
That's right, sometimes the greatest villain in gaming is the person sitting next to you on the couch. Mario Kart and Smash Brothers are to blame for many a villain's origin stories.