In 1988's The Cult, Gotham City's homeless population is disappearing. Batman investigates, and ends up finding an underground army of Gotham's poor and downtrodden, lead by Deacon Blackfire, a charismatic cult leader. Drugged and tortured, Batman is eventually brainwashed into becoming one of Blackfire's followers, even to the point of committing murder while under Deacon Blackfire's spell. Blackfire and his cult take over Gotham, hoping to purge the city of crime by keeping it under the rule of the homeless army. Eventually Batman is freed, and he gets in a Batmobile that looks a lot like a monster truck (see it here at the History of the Batmobile site), and takes down Blackfire and the cult.
Pros: Blackfire's a somewhat interesting villain, in that he appeals to Batman's sense of justice, but he takes it too far.
Cons:The Cult was a controversial story for its violence and gore (decapitated heads, Batman murdering someone, a badly scarred hooker). It's also out of print, I think, so Blackfire is not going to be all that well known. And the central element of his story is breaking down Batman until he's crying like a little girl, which is not exactly consistent with the badass Batman we know and love. The idea of Batman as a superhero to me is that he may not have a superhuman body like Superman, but he has a superhuman will, and seeing someone break that will just doesn't work for me.
How I'd do it: Eh, I don't think I would. But the basic premise of a cult leader recruiting the downtrodden to take back the city works. I just don't know about the brainwashing of Batman.
Casting Guesses: I could see Russell Crowe doing it.
After The Scarecrow, Ra's Al Ghul, The Joker, and Two-Face, who should be Batman's next enemy in the Batman Begins/The Dark Knight series? Well, as of now we know that Tom Hardy will play Bane and Anne Hathaway will play Catwoman.
Check out the master list for all the villains covered. I've pretty much run out by now. Obviously, there are more Batman villains, but not any of significance that I know of. As of February 2009, no one is confirmed as a villain. Not the Johnny Depp Riddler, not Phillip Seymour Hoffman Penguin, nobody.