Bowser and Ganondorf, of course.
Kefka is a pretty fair ways up the list for me; that has to be one of the greatest MIDI laughs ever created, and he was so utterly, utterly cracked that it was hard not to love him (while simultaneously wanting to push his face out the back of his skull). Plus, really, how many villains actually get to blow up the world less than halfway through the game?
G La Dos, of course, just for the marvelous voice acting and the magnificent stream of passive-aggressive taunting.
... huh. For all the games I play, you'd think there'd be more standout villains :/
Villains huh? Well let me see.
- SHODAN- L-l-look at you h-hacker. A-a p-pathe-etic creature of meat and bones.
- Vergil- Might controls everything.
- Alma Wade- I know who you are.
- Ghirahim- You know how that makes me feel? FURIOUS! OUTRAGED!! SICK WITH ANGER!!!
- GLaDOS- For science. You monster.
- Vaas- Did I ever tell you the definition of insanity?
- Revolver Ocelot- You're pretty good.
- Omega- I am the dark messiah! HA HA HA HA!!!
- Handsome Jack- It's cute that you all think that you're the heroes of this little adventure, but you're NOT.
edited 2nd Jan '13 2:53:31 AM by LDragon2
Jon Irenicus from Baldur's Gate II, (voiced by none other than David Warner) the Master from Fallout, SHODAN from you-know-what, and an honourable mention to AM from the videogame adaptation of I Have No Mouth And I Must Scream since he's technically from the book.
Ding-ding! Going down...
Well, he technically wrote the book as well. 
Ellison is pretty much perfect casting in the role.
Mad Scientist Wannabe
The Cyberdemon from Doom. I'm a relative newbie in the Doom fandom, but man do I see why he's so memorable. The first time I played Doom, I must have spent like a week trying to get past him. Boy, he was intimidating. Hard too; before I learned to circle-strafe, my fights with him were pretty much cat-and-mouse affairs, and the cat won more often than not.
Of course, don't you know anything about ALCHEMY?!- Twin clones of Ivan the Great
Rollin' rollin' rollin'
![[up]](https://static.tvtropes.org/pmwiki/pub/smiles/arrow_up.png "[up]"){kind=icon}
x4: Definitely agreed on GLaDOS and Ghirahim.
Also, Hades from Kid Icarus Uprising.
"We're home, Chewie."
Brightness
Raul Menendez. Holy fuck, that guy is disturbing.
PSN ID: FateSeraph | Switch friendcode: SW-0145-8835-0610 Congratulations! She/They
I also liked Alfred Ashford in Resident Evil Code Veronica because he was freakin' insane.
I liked it better when Questionable Casting was called WTH Casting Agency