My list:
1: THE CHAMP: SPAWN FROM SPAWN!
2.Riddick himself (Yeah,he IS a bad guy) from Chronicles of Riddick.
3. Oogie Boogie from The Nightmare Before Christmas.
4.The Clown from Spawn.
5.The Necromonger Lord from The Chronicles of Riddick.
6.Darth Vader from StarWars.
7.The Alien for Alien Series.
8.Predator from Alien/Predator/Alien&Predator series.
9.Martian's from The Matrian's Movie.
BTW,Oogie Boogie is The best animated Villain.Look at he's Intro:
http://www.youtube.com/watch?v=Yw0aoVpFCDw