There are a few significant clock kings out there. First, there's William Tockman, a Green Arrow villain who attempted to rob a bank by memorizing the timing of the bank's operation, only to be stopped by a silent alarm. As a career criminal, Tockman's crimes were always time-themed. This version was also adapted for the 1960s Batman TV series, played by Walter Slezak.
Second, there's a recurring Clock King villain from Batman: the Animated Series. On his way to an important day at work, Temple Fugate is inadvertantly delayed by lawyer Hamilton Hill, and the delay ends up costing Fugate his job. Distraught over the disruption in timing, Fugate becomes obsessed with time, and obsessed with revenge on Hamilton Hill, who had since become Mayor of Gotham. Notable for his precise timing of every event, he's a master planner, so much so that his character returns for a Justice League Unlimited episode where he plans a Suicide Squad raid on Justice League headquarters down to the second.
Third, there's a new Clock King in Teen Titans comic books (pictured above), who apparently can see a few seconds into the future. Obviously, in the wrong hands, this is a powerful and dangerous ability.
Small confession: I've never read a comic book with the Clock King in it. But since the comic book versions of the Clock King are more Green Arrow/Teen Titans enemies, that doesn't really affect the Batman angle.
Pros: There's nothing technically supernatural about the first or second Clock Kings, and someone with that kind of ability to coordinate timed events is very dangerous.
Cons: The Joker's opening heist in The Dark Knight demonstrated a similar planning/timing ability, so that might seem repetitive.
How I'd do it: I rather liked the Temple Fugate character, so if I had to do the Clock King I might just rip off that story completely.
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.