Anton Chigurh (No Country for Old Men)
Joker (The Dark Knight)
Hannibal Lecter (The Silence of the Lambs)
Agent Smith (The Matrix)
Commodus (Gladiator)
Nina Myers (24)
Boyd Crowder (Justified)
Quarles (Justified)
Hans Gruber (Die Hard)
Charlie Prince (3:10 to Yuma)
Lex Luthor (Smallville)
Charles Logan (24)
Kinda hoping The Governor (Walking Dead) and Bane (Dark Knight Rises) make this list in the near future. I skipped a few that are always mentioned.
I'd add: Hellraiser Pinhead, Phantasm Tallman, Human/Alien criminal from "Laserblast", Kraunch from "City of Lost Children", David Bowie in "Labyrinth", Sting in Dune...