My all time favorite bad guys are:
1. Evil Genius from Time Bandits aka Pure Evil.
Evil: If I were creating the world I wouldn't mess about with butterflies and daffodils. I would have started with lasers, eight o'clock, Day One!
[zaps one of his minions accidentally, minion screams]
Evil: Sorry.
2. Xur from The Last Starfighter. He is one of my favorites just because every time he gets mad he has to raise that scepter thing and make the blade come out.
3. Khan from Star Trek II. Hands down best over the top villain.