Luther Sloan, Star Trek: Deep Space Nine
Sloane is an operative of Section 31, an intelligence agency that doesn't exist. He wants to stop the Dominion War at all costs, which usually means defying the letter and spirit of every law on Federation records. What makes him a good villain is his mystery: you never really know exactly what he's up to. He's organized assassinations, turned loyal Starfleet personnel into pawns for his bigger plans, and even after his death he trapped Dr. Julian Bashir and Chief Miles O'Brien in his brain to stop them from trying to peacefully end the war. Sloane's cruelty is matched only by his patriotism for the Federation. For a self-proclaimed good guy, he's quite villainous.
Arvin Sloane, Alias
What is it with the name Sloane? Arvin Sloane is an international terrorist, conspirist, and artifact enthusiast. He runs SD-6, a terrorist organization under the guise of a secret CIA project; thus, all the agents working for Sloane believe they are helping the government, when they are in fact committing acts of terrorism. Sloane fakes his own death and topples the Alliance, an international terrorist organization of which SD-6 was a part of, allowing him to operate freely and beyond their influence. His entire goal in life is to seek all the artifacts of Renaissance artist Milo Rambaldi, a proported prophet who created technologies far beyond his time. To this goal, Sloane will let nothing stop him, abandoning old friends, killing loyal agents, even murdering his own daughter. Sloane does eventually collect all the necessary Rambaldi artifacts to fulfill the prophesy, and he gains immortality in doing so. In a cruel (or just) twist of fate, however, a CIA agent detonantes a string of grenades while they are in Rambaldi's tomb. A boulder falls on Sloane, keeping him hopelessly pinned but forever alive. Sloane's villainy is found in his cold, calculating nature and willingness to sacrifice anything and anyone for his plans.