I love the "villains" that may not really be villians. Javert was the first that came to mind, you understand his actions even though you don't agree with them. I guess you could say the same about the Phantom, but I love the character way too much to consider him a villian.
I guess my other fav would be villians that aren't simply one person but just dimensional. Though Nazis appear to be the villians in Cabaret, I think it's human nature that really is. Same goes for the Constable in Fiddler or the circumstances that affected the Bui Doi in Miss Saigon.
"If there was a Mount Rushmore for Broadway scores, "West Side Story" would be front and center. It snaps, it crackles it pops! It surges with a roar, its energy and sheer life undiminished by the years" - NYPost reviewer Elisabeth Vincentelli