Here are some of mine:
Alonzo Harris - Training Day
Lumburg - Office Space
Brick Top - Snatch
Mister - The Color Purple
Begbie - Trainspotting
Hans Gruber - Die Hard
Sokourah the Magician – Seventh Voyage of Sinbad – Torin Thatcher
Wonderful performance, very menacing
Auric Goldfinger – Goldfinger – Gert Frobe
The best Bond villain -- he takes childish delight in showy presentations, even when he's going to kill the presentee.
“The Jackal” – Day of The Jackal – Edward Fox
Tough, smart, no-nonsense methodical killerNurse Ratched - One Flew Over the Cuckoo’s Nest
Begby - Trainspotting
“Reverend” Harry Powell - Night of the Hunter
Snow Queen - the Lion, the Witch & the Wardrobe
Count Graf Orlock - Nosferatu (1920s version - creepiest vampire ever)
Count Graf Orlock - Nosferatu (much under-rated 70s version - a close second)
and of course…
KHAN!!!
Off the top of my head:
Margaret Hamilton as the Wicked Witch in The Wizard of Oz
Billy Zane (can’t remember his character’s name) in Titanic
ETA: Zane was freaky in Dead Calm, too
Darth Vader in the Star Wars series
Jeremy Irons was delicious as Scar in The Lion King
Nobody is badder than Darth Vader. 2 movies of true evil. (There were never more than 2. Ever.)
Alan Rickman!
Especially as the Sheriff of Nottingham.
My little-known choice:
Dawg Brown - ** Cutthroat Island**, played by Frank Langella.
Max Shreck in **Batman Returns ** (well…any Chris Walken)
Maleficent in Sleeping Beauty
Oooo yes… most definitely!
Hans Gruber is by far the best villain.
The iceberg in Titanic.
That cold hearted killer took that dork DiCaprio down and let me go home. That block rocks!
Simon came a close second, though. I’ve always wanted to see a movie spun off of Die Hard that centered around the Gruber brothers working together.
Thulsa Doom, Conan the Barbarian, James Earl Jones.
He calls a pretty girl to willingly & knowingly leap to her death, just to impress a thief before having him executed.
Now they will know why they are afraid of the dark. Now they learn why they fear the night.
Hannibal Lechter The Silence of the Lambs.
A terrifying man even when he’s not doing anything.
I’ll echo this one and follow up with Alan Rickman or Gary Oldman in any villain role they’ve ever done. 
Leon The Professional, The Fifth Element, Robin Hood, Quigley Down Under, and Die Hard all come to mind.
Oooh – good one. But I’ll also nominate Cox’ interpretation (before Hopkins’) in Manhunter. The way he could manipulate people from inside his cage was wonderful.
Emperor Palpatine
Hans Gruber, of course
Humperdink from Princess Bride
Kaizer Soze from The Usual Suspects
Goldfinger (James Bond: Do you expect me to talk? Goldfinger: No Mr. Bond, I expect you to die!)
King Ming and his snake Klytus from Flash Gordon
Norman Bates
Damon Killian (Richard Dawson, the evil game show host in The Running Man)
Darwin and Mynerva Mayflower (Richard Grant and Sandra Bernhardt in Hudson Hawk)
Dean Wormer in Animalhouse
Longshanks in Braveheart (Prima Nocte. If we can’t get them out, we’ll breed them out)
Tim Roth in Rob Roy - All he had to do was walk on camera and smirk and I wanted to beat the shit out of him.
Ciarán Hinds in the BBC miniseries of Ivanhoe - The performances in this version of the story were excellent all around, but Sir Brian duBois Gilbert packed more acting into every second of screen time than everyone else combined.
Siân Phillips, John Hurt, and Patrick Stewart in I, Claudius - To name a few. Thirteen hours of debauchery that only the Old Testament could possibly match. Declaimed by the finest cast that upper-class England could conjure.
Eli Wallach in The Magnificent Seven - I lived on the Mexican border for 20 years, and only recently learned that the leader of the banditos was a Jewish guy from New York. :smack:
Yul Brynner in The Ten Commandments - So let it be written. So let it be done. I’m completely straight and that smoldering look makes me quiver.
Ann Baxter in All About Eve - Never did evil – well, ruthless ambition, anyway – inhabit such a lovely face.
Victor McLaglen in The Quiet Man - Not a hissable villain, I’ll admit. But I’ve never seen the small town bully played better.
Jean Hagen in Singin’ In The Rain - “Wha’d’ya think I am? Dumb or somethin’?” Lena Lamont served as a perfect example when I set out to teach my daughter that “beautiful” is all well and good, but is not the end beat all of personal qualities.
John Malkovich and Glenn Close in Dangerous Liaisons - And you wonder why these people all head their heads chopped off by angry mobs?
Bruno Ganz in Der Untergang (Downfall) - This one tops them all. Having watched Og-knows how many WWII documentaries on the Hitler Channel, I couldn’t believe how convincing this guy was. Terrifyingly authentic.
Javier Bardem in No Country for Old Men. There’s a new villain in town.