I find it hard to choose any one villain, so I'll pick a few.
The Auditors: What can you do when the laws of physics personified decide that you need to die?
Ipslore the Red: It's not just that he cheated Death, or decided to plunge the Discworld into a war that could have very well destroyed it. He mentally rapes his son.
The Archchancellor's Hat: More mental violation and megalomania.
Vorbis: Rewrites his own personal reality inside his head, believing his own BS.
Teatime: Obvious, isn't it?
The Cunning Man: No eyes, makes people hate witches, and basically makes people hate everything.
The Doctor: There's one thing you never put in a trap, if you're smart, if you value your continued existence, if you have any plans about seeing tomorrow, there's one thing you never, ever put in a trap... Me.
-Doctor Who: The Time of Angels