Good topic, but I'm having difficulties thinking of some examples, too.
One of my first ideas was the T-800's theme for The Terminator; the T-1000's theme was good too.
Superman's "The March of the Villains" is delightful, but does it qualify for the least? It's not exactly "The Imperial March"-- Williams' pizzicato variation for "Darth Vader's Death" is most beautiful, by the way.
Christopher Young's "Birth of The Sandman" was just as delicate and superb-- the character was not meant to be considered utterly evil, but he still was a villain.
Speaking of Williams, there's an obvious one: Jaws' theme for the mayor-- er, the shark, I mean.
Isn't the cool guitar theme from Zimmer's Broken Arrow the villain's theme? I remember reading in the notes he found it important to have a great theme for the villain (not just for this movie, speaking generally).
I cannot pinpoint his theme for Hannibal Lecter, but Zimmer's whole score for Hannibal certainly is most beautiful.
Oh, I've just thought two great ones in one movie: Goldsmith's Klingon theme, introduced at the beginning of Star Trek-- The Motion Picture; wonderful! And then, of course, V'Jur's blaster beam theme is literally awesome.
Schifrin's "ethereal siren vocals" for Dirty Harry's villain (I forget his name) are very cool.
Ah! Another one: "The Gremlins Rag"! (Durn if I can recall the movie's title, though
) It perfectly captures the Gremlins' mysteriousness and impishness.
More Goldsmith gems for villains: Basic Instinct!
And Alien! I could not hum you an exact theme for the Alien, though, come to think of it.
How about Steiner's King Kong?
Danny Elfman's Sleepy Hollow features a gorgeous theme for the Headless Horseman / evil / mystery.
I also particularly like "This is Slade" from Broughton's Mark Twain's Roughing It
Going through the music I have copied onto my laptop, I have found another splendid villain theme/motif: Hector's, from Bernstein's Saturn 3-- which I can't believe I have not played in quite a while; I need to play it soon.