I read the Dr. Light rape story a while ago, so I don't remember how good it was, but I think the idea is sound. What do you do when a supervillain goes that far? Unfortunately, judging by my vague recollections and the complaints of others, the execution was flawed.
Typically, I think the supervillain should be evil in a way that makes for the most interesting story. A mercenary like most of the USM villains is okay every now and then, but frankly I don't even count them as villains. They're just plot devices with no personality. A villain who mass-murders or rapes puppies has their place in a story, but I think the best villains are either A: the kind who are tactically evil, who does incredibly twisted things that are precisely calculated to hurt the hero the most, or B: the kind whose brand of evil challenges the hero's own ethics.
To conclude this post, I leave you with a ****ing awesome quote on the nature of evil from one of the Order of the Stick prequels: