I've talked about religious and political systems a bit. I'm going to toot my own horn a little bit and talk about what I consider the ideal moral system for supervillains. Without further ado, here's Mr. Big's Code of Villain.
The supervillain's first duty is to know how to fight. All other rights or privileges may be removed by force, and can ultimately be defended by force. Know when not to fight, but be prepared to fight anyway. Knowing the proper use of your powers is part of effective fighting.
The supervillain's second duty is to his good name. Your reputation will compel respect or mockery, love or fear. Honor your word whenever you've given it. Never give your word unless it's the only price that will buy you what you want.
Don't kill the goose that lays the golden egg. Don't draw all the water from the well. Sooner or later, you will need the civilian population, the local economy, your friends, your enemies. Give, when you can afford to be generous. Take, but do not exhaust. Commit crimes, but not atrocities.
Be respectful of the powerful. Be understanding of the weak. You have a place in the world's hierarchy. Move up it whenever you can, but don't force yourself or you'll regret it.
Aside from these things, there's the two-word advice I give to any aspiring supervillain, or anyone else for that matter:
Be practical. If something isn't working, stop doing it! If what you're doing now isn't working very well, try something new!