Meh. Some of my favorites that hadn't been mentioned:

From books:
Lord Voldemort - Harry Potter
Sauron - Lord of the Rings
Morgoth - The Silmarillion
Cyric - various Forgotten Realms novels

From movies:
Commodus - Gladiator
HAL - 2001
Imhotep - The Mummy movies

From cartoons:
Megatron/Galvatron - The Transformers
Skeletor - He-Man
MumRa - Thundercats
Dr. Claw - Inspector Gadget
Prince Lotor - Voltron
Serpentor - GI Joe

Disney villains:
Maleficent

From games:
Ganon(dorf)
Sarevok - Baldur's Gate 1

Two of my favorite villains are not so much diabolically evil as extremely selfish:
Jon Irenicus - Baldur's Gate 2
The Transcendent One - Planescape Torment