My favourite villains? Hmm well....
Anime
Crocodile - One Piece
Marshall D. Teach (Blackbeard) - One Piece
Donquixote Doflamingo - One Piece
Schneizel el Britannia - Code Geass
Movies
Hannibal Lecter - The Silence of the Lambs
Darth Vader - Star Wars
Palpatine - Star Wars
Ozymindas - Watchmen
Colonel Hans Landa - Inglourious Basterds
The Duke of Norfolk - Elizabeth
The Joker - The Dark Knight
Ra's al Ghul - Batman Begins
The Scarecrow - Batman Begins
Jackson Rippner - Red Eye
Norman Stansfield - Leon: The Professional
Amon Goeth - Schindler's List
Lord Summerisle - The Wicker Man
Karl Ruprecht Kroenen - Hellboy
Prince Nuada - Hellboy II: The Golden Army
Hans Gruber - Die Hard
Norman Bates - Psycho
Captain Vidal - Pan's Labyrinth
Mr. Blonde - Reservoir Dogs
John Doe - Seven
Agent Smith - The Matrix
TV Shows
The Hands of Blue - Firefly
The Daleks - Doctor Who
The Master (played by John Simm) - Doctor Who
The Weeping Angels - Doctor Who
Alpha - Dollhouse
Disney and other Western Animated Media
Judge Claude Frollo - The Hunchback of Notre Dame
Scar - The Lion King
I'm not quite sure where I would be these people in terms of category. I had to stop myself from putting "villains" here because they were hot and just happened to be evil. A great deal of these people are here because they quite honestly scare me. Like the Daleks and the Weeping Angels, of course, but also Amon Goeth and John Doe. But almost all of these people are here because they are just great at being completely and ruthlessly evil and vile and horrible people. Bonus points if they manage to chew the scenery while being evil.
I'm genuinely surprised that Judge Frollo isn't in the Disney(ish) picspam of villains. He surpasses almost everyone in his fanaticism, his cruelty, and the sheer horrifying series of actions he takes. He kills a mother and tries to drown her baby within five minutes of the movie, for heavens' sakes. And lest we forget, he has one of the coolest songs ever.
Hellfire
Do we have a section for anti-heroes? Like extreme anti-heroes? Like Lelouch vi Britannia. He has such an impressive evil laugh.
EDIT: Oh drats! I forgot Dr. Horrible. Who has a Ph.D in horribleness.