For confirmed villains, I suppose either the Dragon from Guards! Guards! or Carcer. The Dragon because of its nigh-invulnerable corruption of Ankh-Morpork, and Carcer not so much because he's a shameless psychopath but because he tries his best to look innocent, which is just insecure.
For ensembles, it's between the Cable Street Particulars, the Omnian torturers, or the Elves. All of them do the same gruesome acts on people, though for different reasons.
For "potential" villains, Granny Weatherwax gone bad is a scary thought.
"The truth shall make ye fret."