Geoffrey Rush as Cassanova Frankenstein in Mystery Men and Captain Barbossa in Pirates of the Caribbean although those were pretty much the same character
John Malkovitch also plays effective rat bastards in Ripley’s Game and Mary Reilly…
The jewel thief movie is The Object of Beauty, probably.
Mike Myers played two great villains in ONE FREAKIN’ MOVIE!
Ronnie Cox was a great slime in both Robocop and Total Recall.
In Robocop, as Dick Jones:
"I had a guaranteed military sale with ED209! Renovation program! Spare parts for 25 years! Who cares if it worked or not! "
in Total Recall, as Cohaagen:
“I have the greatest job in the solar system. As long as the Trebinium keeps flowing, I can do anything I want. ANYTHING.”
Robert Mitchum in Night of the Hunter and Cape Fear. He scared the crap out of me in both.
Although he’s been trying to get away from such roles since he won the Best Actor Oscar, Kevin Spacey has played (or, in one case, voiced) a number of memorable villains on TV (Mel Proffit on “Wiseguy”) and in the movies Seven, A Bug’s Life, Swimming with Sharks, and The Usual Suspects (since you didn’t find out until the end).
Another John Lithgow villain was Burke, the ultimate political dirty trickster in 1981’s Blow Out.
Quite a few actors who later became better known as leads actually started out as memorable villains:
Ernest Borgnine – From Here to Eternity, Bad Day at Black Rock, Johnny Guitar
Broderick Crawford – All the King’s Men, Born Yesterday
Lee Marvin – The Big Heat, The Man Who Shot Liberty Valance
Jack Palance – Panic in the Streets, Shane
Richard Widmark – Kiss of Death, Street with No Name, No Way Out
Elisha Cook, Jr. – always memorable, though he usually played the same sort of character.
And what of Quigley Down Under with Tom Selleck. He was the rancher hunting aboriginies with a delusion of cowboy-ism
Oh, and another Christopher Lee baddie: Wendell Wonka, D.D.S.
He also played Top Dollar in The Crow.
Two posts about Michael Wincott and no meantion of Top Dollar from The Crow?
Then there’s this guy called Al Pacino :
The Recruit-Walter Burke
The Devil’s Advocate-John Milton/Lucifer
Heat-Lt. Vincent Hanna…well that’s just me
Scarface-Tony Montana
Dog Day Afternoon-Sonny Wortzik
And the surprisingly eerie Robin Williams :
Insomnia-Walter Finch
One Hour Photo-Sy Parrish
If you say he was good in it, I will believe, but I couldn’t sit through this movie. I don’t remember him in it.
I kick myself for not immediately mentioning Bruce Dern. He’s been made a career out of being a badass psycho in movies like The Cowboys, Tatoo, Hang 'em high, Black Sunday. The list is endless.
Oh come on- his Ygor in the Frankenstein films (SON OF and GHOST OF) was great, and even tho it was for Ed Wood, his heart really was into the mad scientist in BRIDE OF THE ATOM/MONSTER - “Home? I heff no home…”
RE Chris Lee-
Wendell Wonka wasn’t a villian- just very overprotective.
However-
the Frankenstein Monster (no sympathetic creature here- HE MURDERS THE
OLD BLIND MAN!)
the Mummy
and Lord Summerisle in THE WICKER MAN!
Given that elsewhere on the board, people were actually positing Mother Teresa as the most evil woman of the 20th century, perhaps not! 
Anthony Hopkins-
Hannibal Lecter
Hitler
and to some Dopers, St. Paul! again
Point of order…Pacino’s not a villain in Dog Day Afternoon…he’s a criminal, but he’s the most likable character in the movie: he’s more of an “anti-hero.” (Whether he’s an anti-hero in Scarface would take some debating.)
Same goes, by the way, for the earlier votes for Cagney in Angels with Dirty Faces and The Public Enemy. And is Alex in A Clockwork Orange really a villain?
I agree except Alex was a villain as was everyone in Clockwork Orange. Same was true of book. Everybody was out for themselves, everyone was villainous.
Some of these posts are questionable to me as great villains. I know Michael Caine has played villains but were they great?
I also wouldn’t call Lithgow’s villains great or even scary.
But I’ve seen lots of great examples so far.
The Dark Side clouds everything.