On Dr. Horrible and the nature of villainy

This is a post I've been meaning to write for some time, but then NaNoWriMo occupied me and I forgot about it for a while.  Anyway, here it is!

Recently, Shelly of 20sb alerted me to the awesomeness that is known as Dr. Horrible's Sing-Along Blog.  You can find this on Youtube, so I leave the rest up to you.  It really is worth it.  Anyway, after viewing it, I got thinking about the nature of villains in fiction.  Writing a villain is relatively easy, but writing a convincing, compelling villain is much harder.  The trick to this is in realizing that our stories are not old-fashioned melodramas.  Unless your villain is the devil himself, he probably doesn't wake up each morning plotting new ways to confound your hero.  I think the best way to look at the situation is not to think of it as antagonism, but more as people at cross-purposes.  The key to this is that whatever their motives, the villain always believes that what they're doing is right, however wrong it may be.  Furthermore, there are probably very good reasons for them to act and think in this way.  When the reader discovers these motivations, what first looked like a chaotic murderer may seem perfectly logical in their actions.  This is not to say that the reader should want the villain to succeed, of course, but understanding what makes the villain tick (even if you reveal only a small part of their character) makes them much more fascinating to read about.  In point of fact, the villain is most often far more interesting than the hero.  For instance, what would Batman be without The Joker?  Granted, we don't truly understand everything about The Joker, but we know enough, and that's what makes it so compelling to read.  (see Alan Moore's The Killing Joke for further examples)
To summarize, all characters are human (even if they're aliens), and it's their human nature that makes them interesting to read about.  Villains are the heroes in their own minds.