To say the least, my favorite villains are:
1) Ganon from Zelda: Ocarina of Time
He was such a bad ass and loved to destroy all the land (Hyrule) around him. He originally was a theif from the bad land area (cant remember the name right now) and wanted to own the TriForce. Truely the worst villain ever

2) The Covenat- Halo 1 and Halo 2
Somebody on this forum knew that one of us Dragoons would post this. Religious war agains humans when we didnt do anything to start the war??? All these weapons and all of this trying to take over earth. Good job assholes.

3) Bowser- Mario Series
I dont even have to explain this one because a dinosaur spitting fire is not worth enough of a description