I read once that the greatest villains are the ones that truly believe they are doing the right thing.

Great topic for discussion. It's actually something I've thought a litle about myself, though mostly because of an upcoming television show called Heroes. It's supposed to be about normal people that find themselves coming into various superheroish powers.

I definitely don't think the hero has to be your main character. That's typically the way things are written of course, but I know there are examples where the main character may, in fact, be the villain. Or, perhaps the main character is simply an incidental, a bystander that is affected by the hero's actions.

I read an entire chapter on this topic actually in "How to Write Science Fiction & Fantasy" by Orson Scott Card. It was a book that kept me from boredom during my stint on jury duty at the beginning of the year! I highly recommend it for anyone interested in those genres.