Waiting for the Worms (Pink Floyd, The Wall) - Yes, Pink isn't technically a villain, but this is a side of him he doesn't like. It's sort of a Man vs. Self motif, so I hope you'll accept it.
Be Prepared (Scar, The Lion King) - Good chance someone else will nominate this, too, so I'm just throwing it out there.
Special (Lucy the Slut, Avenue Q) - Here's one song the singer has to own in order to make it work. I like Julie Atherton's rendition with the faux Southern drawl.