The Doomsday Machine
Yes, we know: the Doomsday Machine, as first seen in the 1967 episode of the same name, is technically more of a mechanical menace than a villain, per se. But come on – this is one scary contraption. It's a flying weapon of mass destruction that roams through space, chewing up planets and starships everywhere it goes. (So, basically a Death Star, 10 years earlier. Sorry, Star Wars fans.) Just seeing it is enough to drive high-ranking Starfleet officer Matt Decker mad. Can you really blame him?