Lord Vetinari, if you can count him as a villain, closely followed by GLaDOS.
I personally wouldn't call Vetinari a villain. The only people he has killed are the ones who need to be killed for his city to run smoothly.
Heath ledger as the Joker, Javier Bardem as Anton Chigurh, Chiwetel Ejiofor as The Operative, Richard Brooks as Jubal Early, Cliff Simon as Ba'al, Juliet Landau as Drusilla, Tom Hiddleston as Loki, Christoph Waltz as Col. Hans Landa, Christopher Lee as Saruman and many others that I can't remember at this time.
For books I would say Flagg, Thrawn, Deacon Vorbis and some others that I can't really remember right now.