For some reason, I've been thinking about Batman a lot lately.
Despite Christopher Nolan's best efforts to bring that universe into something resembling reality, there's no doubt that the villains are pretty ridiculous. However, as with Tolkien's Mt. Doom, those characters are now so well known that no one seems to notice how fairly stupid they are. I'll let you mentally run through the roster on your own, but here's a preview: one of them is a PENGUIN MAN.*
That being said, Batman's little circus of evil weirdos has taught me a lot about what makes a good villain. In terms of storytelling, the purpose of an enemy is to reveal the hero-to challenge the champion in interesting ways, force him to make interesting choices. The way you equip a good enemy to do that is by making him a foil for some virtue of the hero.
Riddler - Intellectual foil
Catwoman - Physical/Stealthy foil
Mr. Freeze - Technological foil
Scarecrow - Foil for Batman's use of fear
Joker - Foil for Batman's will, his capacity for taking actions that other people don't.
These enemies all do something that Batman does, but usually better, and that keeps Batman's abilities from seeming unstoppable, while also forcing him to use the rest of his arsenal in new ways.
*And another one is a ventriloquist. Yeah.