Harry Lime from The Third Man
Nobody’s mentioned Evil Genius from Time Bandits yet?
Close enough, still one of the most effective antagonists. And one of the big questions the film poses is whether HAL 9000 has reached an equivelent level of intellectual and emotional intelligence as humans. I would argue that human psychology is a factor.
If we take non human psychology into account you will have to rule out any robotic computer oriented villains such as the Terminators, Borg, or certain fantasy figures.
Most effective villains are victims of circumstances, those who are not are usually two-dimensional. I’m not a huge fan of villains who kill just because it’s what they like to do. There needs to be an understanding of where that motivation comes from.
Cyrus theVirus from Con air…
Three quick ones (I’m supposed to be working!)
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Donald Sutherland in Eye of the Needle - He kills who ever gets in his way, just like <snap>that!</snap>. No fuss, no speeches, just murder.
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Orson Welles in The Stranger. A realistic, and really scary, Nazi-on-the-lam flick. It was released in 1946, when Nazis-on-the-lam were not cartoonish, just evil.
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James Cromwell in LA Confidential. Yes, Farmer Hoggett is a stone killer. His eyes are cold.
A great one, in an underappreciated movie. “Never underestimate the healing power of hate.”
One of my favorite movie villains is the Dr. Charles Nichols character in The Fugitive.
An elegantly dressed, obviously well-heeled pathologist who has clinicians hanging on his every word (dream on, Jackmannii), he was also Richard Kimble’s nemesis and generated the most unintentionally hilarious line in the movie. This was when he was addressing the cardiologists’ convention and told them that the new heart drug was wonderfully effective and had absolutely no side effects whatsoever. (In real life, any such claim would have generated a moment of stunned silence, followed by guffaws and catcalls).
Ming the Merciless from the 1980 version of Flash Gordon – no ambiguities here, just pure tyranny, greed, lust and malice! The real thing!
I’ve always gone back to the uber-smooth bad-guy Lord Wolfingham, in the 1940 film The Sea Hawk. Played to the absolute peak of human villiany matched with an aloof aristocratic charm, as portrayed by Henry Daniell.
The charactor was given an homage as **Count Tyrone Rugen ** played by Christopher Guest in The Princess Bride.
But Hans Gruber comes damn close.
And from Babyon 5, we have the cold-blooded Machiavellan Lord Refa; the gloriously over-the-top Caligulan Emperor Cartagia; the Mephistophelian Mr. Morden; and the telepath-supremacist fascist megalomaniac Alfred Bester. There’s some villains for ya! (That’s about it, really. The Shadows figure as monsters, not villains, and President Clark never develops as a character.)
Bosda already offered Nicholson as The Joker, albeit in light of seeing only very brief footage of Heath Ledger in the role, I think he could become the greatest comic book villain adaptation ever. I thought he had no hope but he has totally disappeared into the role. He’s my new favorite villain and I haven’t even seen the movie yet. 
Michael Caine in Quills. I’ve never wanted to punch him in the face before, but I did after that one.
A fantastic performance (one of many in a great movie), but that’s a bit of a spoiler. The fact that he’s a villain comes as a major twist over halfway through the movie.
Professor Fate in The Great Race.
For me, the ultimate all-time movie villain is the Scorpio Killer from Dirty Harry, played ingeniously by Andrew Robinson. The character was so loathsome and vile that Robinson received many death threats and had to change his phone number. I think that says it all.
On a lighter note, William Zabka as Johnny Lawrence in The Karate Kid is pretty hard to top for the teen-movie genre. A close second would be James Spader’s character in Pretty In Pink. Love those rich, blond, smug yuppie-kid villains.
On that note, I must link you to the following:
http://www.sweeptheleg.com/
I’ve seen that - it’s hilarious.
SID 6.7 (played by Russel Crowe) in Vituosity was awe inspiring. The movie itself wasn’t, but Crowe was.
“Perhaps I’ll hang him … by the balls.”
Ben Kingsly as Don Logan from Sexy Beast. Watched it again recently, and it was as good as the first time.
“Get off the bed!”