Kane from C&C was already mentioned he takes my number one spot for just being one of the most cunning and intelligent villians I've ever seen.
Cobra Commander not from the old Gi-joe, the newer Renegades series, he kinda reminded me of kane a bit.
basicly this cobra commander is dying of old age and disease, having single handedly built cobra into a world wide group and terrorist superpower, he's facing his own subordinates, trying to keep the sharks from smelling the blood in the water so to speak. at the same time he's trying to push for a cure, and keep the US military in the dark.
Then these joes stumble across his lab and fuck up his bio-viper project, and nearly expose cobra's dirty underbelly to the world.
he actually acts like the head of a "ruthless terrorist orginization" instead of his bumbling, buffoonish 80's counterpart.
other villians let me see...
in terms of pure and simple evil Soron from the Lord of the Ring's trilogy, not the movies, but the way he's described in the books as a sort of evil mind without a body that's been festering, and the only thing that prevents him from going to the afterlife is a ring, his one weakness. a being that casts a dark shadow across the land even beyond death, who's corruption tears down the greatest wizard of the era, playing on his desire for industry and greed, who controls all the dark things across the land wild and tame, and twists everything... and the battles were freaking brutal in the books, straight out of WW1.
Aragon and the heroes fought him not to win, but all as a distraction so that somthing so small... a pair of tiny hobbits. Could carry his anchor into the heart of his empire and destroy it.