I love most of the villains of SNK's fighting games (at least from the 90's).
Mr. Big from Art of Fighting, Wolfgang Krauser and (the almighty) Geese Howard from Fatal Fury, Goenitz and Orochi from The King of Fighters... They are all awesome in both design and attitude.
But my vote for favorite villain/antagonist in a video game has to go to
Rugal BernsteinIn a way, he is an amalgamation of the powers of some of those characters combined with the arrogance of the others.
Rugal is simply,
THE KING OF FIGHTERS for me (pun intended)!
"Repeat this after me, I'll never take on a GOD again."
PS: I'm also a fan of M. Bison (Vega), Heihachi Mishima and Cervantes de Leon.