There's a line between evil and bad. The best example I ever heard - which came, oddly enough, from a science fiction dog - was that Evil was hurting someone who hadn't hurt you or when hurting was not required.
Dr. Horrible stole the Wonderflonium which is bad, criminal but not evil (I think we'd all agree that while Mal Reynolds could be bad, he wasn't evil). He attempted to unseat the rightfully elected leader of the people at the Town hall which is bad, but not Evil (What's that saying? When treason prospers then none dare call it treason). The whole 'killing' thing can be argued both ways. He had an opportunity to kill the man he hates most in the world but didn't, and maybe even couldn't, do it. That's not evil. Taking his place in the ELoE after
Captain Hammer caused Penny's death could be viewed as both unethical and immoral but not Evil. He may not even have realised what he was doing at the time if he was too traumatised.
The Doctor's whole game plan was to take over the world and make it a better place. I'd say that's a good goal, even if it involves some sundry naughtiness along the way. To my mind he's more Han Solo or Mal Reynolds than The Emperor or Adelai Niska. In fact, under my initial description, Captain Hammer would fall into the Evil category.
And y'know what? It occurs to me that I'm taking this waaaaay too seriously.
Ummm.... Wibble?
http://www.youtube.com/watch?v=2nAuL4gyevQ
