The Joker (TDK) and The Green Goblin of Spider-man would be my top two. The reason here is because these two don't have any typical, materialistic goal in mind. Rather, both fully embrace what it means to be the Villain. To accept that role and fully take it up as one's lot in life, with all else ancillary. These two stand head and shoulders above the rest. They fully personify what it means to exhume the darkest part of people's souls and put it on a pedestal for all to not only see and accept, but to take pride in as well. They exemplify that there's a difference between truly being a villain, and being a run of the mill antagonist.
Sauron and Darth Sidious also fall into this archetypal category. However, while Sauron may be acutely aware of his opposition to the powers of good, Darth Sidious is willing to do great evil in order to achieve a greater good - order and balance in the galaxy. Vader, likewise, while not as much of a Machiavellian, is still quite cunning and likely the greatest warrior that mythos has ever seen. With all of the talk of a "winning ticket" thrown about with November fast approaching, in terms of Villainy, the Sith truly had one. The most cunning strategist and the most deft combatant combining their forces to seize and secure power.
Back to Sauron for a moment... a being second only in power to the gods (Valar), he was arguably the most brilliant, exemplified not through a desire to destroy life, but to dominate it. Yes, he did seek the complete and utter destruction of Men, but he only sought to raze the World of Men in so far as Men were a nuisance that didn't fit into the grand plan. Having clandestinely brought about their downfall with Numenor years earlier, in the LotR tale, he was simply wrapping up unfinished business to enact his complete and utter domination of all life. His servant the Witch-King ended the line of Kings, led the assault on the Minas Tirith, slew Theoden, and the list of his infamy is almost as lengthy of that of his master. Saruman, also a great villain, surrendering his principles for the sake of his own ends; however, he only came onto the scene as a villain once his mind was twisted by Sauron.
I could go on and on, but rather than dwell on every single one, I'll leave it with the diatribe on the above Paradigms of Villainy, as I'll call them, and move on to some other favorites.
Daniel Plainview - "There Will Be Blood" (though he's also the protagonist)
Scar - "The Lion King"
Hans & Simon Gruber - "Die Hard" & "Die Hard with a Vengeance"
Barbossa & Davy Jones - "PotC"
The Joker - "Batman: The Mask of the Phantasm"
Ra's al Ghul - "Batman Begins"
Hannibal Lecter - "Silence of the Lambs", "Hannibal", "Red Dragon"
Magneto - "X-Men", "X2", "X-Men 3: TLS"
John Doe - "Se7en"
Anton Chigurh - "No Country for Old Men"
Norman Stansfield - "Leon: The Professional"
Lex Luthor - "Superman Returns" (movie was crap, but Luthor was good)
Sloan - "Wanted"
Col. William Tavington - "The Patriot"
Voldemort - "Harry Potter"
Megatron - "Transformers"
Boba Fett - "Star Wars"
Frank Costello - "The Departed"
Commodus - "Gladiator"
Bill - "Kill Bill"
T-1000 - "T2"
The Dark Planet - "The Fifth Element"
Sid 6.7 - "Virtuosity"
Vincent - "Collateral"
Viktor - "Underworld"
Agamemnon - "Troy"
The Jackal - "The Jackal"
Agent Smith - "The Matrix"
Khan - "Star Trek II: The Wrath of Khan"
Thade - "Planet of the Apes"
Cyrus "The Virus" Grissom - "Con Air"
Thulsa Doom - "Conan the Barbarian"