While he's not actually my favorite, I'd like to put a word in for Golbez. Sure, he's kind of a Darth Vader ripoff (which only makes him more awesome, now that I think of it...), but he's also the only videogame villain I can think of who never loses to the player. Not once. At best, you manage to survive a fight with him, but in the end he still walks away from the battle with whatever his goal was.

Kain from legacy of kain series

It really is Kefka no contest.

Dr Eggman

That's not what your sig implies...

Visari and Radec

i have to say either
the panther king(funniest villain ever)
professor pester(i have to mention the pinatas)

Collosi #13 and #16

Ganondorf-fantastic villain, best in Ocarina of Time, I think. I was a bit disappointed with him in TP-his design was fantastic, as were the fights against him, but plot-wise it doesn't do much for me.

Galcian from Skies of Arcadia, another manipulative and very cold character, a great villian in a great game.

Edit: Have to add Bowser, of course, I thought his most menacing appearance was Galaxy, he looked stunning and even if the boss fights were repetitive, they were quite a specatacle.

Other than those... I struggle to think of truly memorable videogame villains. Saren is great in Mass Effect, his appearance, voice and theme exude atmosphere and menace. The development of his motives through the game is also enjoyable and interesting. Also, Sovereign in Mass Effect is pretty cool, even if it isn't prominent for large parts of the game.

Sephiroth, Wesker, Liquid Snake, Pyramid Head, Ganondorf, Bowser, Dracula, Locust Queen...There's a lot more. I can't think of anything else.