There are half a dozen AU snippets on the kink meme where Holmes is a criminal, and part of me is certain there should be, somewhere, an epic AU that goes that way, however I have not yet come across it.

Watson could be the particularly cruel doctor-sidekick, who knows how to kill people quickly, or torture them as slowly as possible. Or perhaps the doctor-turned-detective trying to track him down, and there could be fo-yay.