For all that I'm not a Fantastic Four fan, Doctor Doom has to make anyone's short list of best villains. Not just for his sheer power and all-encompassing knowledge, but because he's got STYLE. Who else could pull off that clunky gray armor and green cloak look without looking stupid?
Speaking of the FF, the Four from Planetary are pretty scary, both in their power and their arrogance. It's been a long time since I ever believed a villain was unstoppable, but I believe it of them.
Other notables: Tyrion Lannister from George R. R. Martin's "A Song of Ice and Fire" series, Doc Savage's nemesis John Sunlight, Uriah Heep of David Copperfield, Rupert von Hentzau from The Prisoner of Zenda, George MacDonald Fraser's Sir Harry Flashman, the Dominator from Glen Cook's "Black Company" series (gotta appreciate a guy who can scare his enemies shitless even when he's dead), the Mayor from Buffy the Vampire Slayer, Triple H (at least from late 1999 to 2000), Shakespeare's Iago and Richard III ... I could probably go on all day.