I think Giovanni's the most sinister... He's not just some madman out to rule the world... he's actually got a plan and has invested a good amount of time/resources in training pawns and building facilities all over Kanto/Johto, it seems. Not to mention the whole Mewtwo thing... Running a gym AND being the leader of a massive crime organization that aren't just environmentalists gone insane? XD Pretty good cover, i guess. That and he's the boss of most of the other "villains" that appear in the anime. Unfortunately for all of the villains, Pokemon also seems to be becoming more and more light-hearted as we go... o__0
Butler was just... revenge-happy. XD And misunderstood and kinda crazy. He WAS dark at first, i guess, but he turned out good in the end...