I agree with the Speculalist review that Dark Knight is a Godfather calibre movie
Batman from the comics has a large collection of high quality villains. The best villains for the Christian Bale Batman would be ones with action and those who would create emotional, moral and psychological challenges. The villains also need to be adapted to be believable, which is more a writing challenge and how they are approached rather than something exclusively in the concept of the villain characters.
Catwoman : One of the primary love interests for Batman in the comics. An action character who is emotionally and romantically tempting.
Talia al Ghul and the remainders of the League of Assassins: Daughter of Ra's al Ghul (Batman Begins). There would be interesting plot dynamics here, but they would seem to be repeating Batman Begins. So there would need to be 2-4 movies done with other villains before going back to this well.
Hugo Strange: Strange is an insane psychologist who knows Bruce Wayne's secret identity and lusts to take the identity for himself. He is also a chemical genius who can turn people into lumbering, brutal giants.
A plot would get to delve deeply into the motivations of Batman and a very close pretender to Batman.
Clayface : Cinematic face changing look. Could be just adjusted to be just a master of disguise. Probably a better secondary villain whose abilities makes it more difficult for Batman to defeat a primary villain.
Hush: A childhood friend of Bruce Wayne's, Thomas "Tommy" Elliot targets both Batman and Bruce Wayne. Hush uses manipulation and guile instead of noisy "signatures".
The Riddler : Already being tipped as the primary villain in the next movie. A good movie would focus on the mind games.
Joker: He is used again and again in the comic books and can be brought back in the movies as well.
Bane: Would need to be made more psychological interesting for a good movie. King Snake is a martial artist who becomes a mercenary, who was Bane's father in the comics.
An escaped convict from an island prison in South America, Bane has abnormal strength as a result of having had experiments with a derivative of the drug Venom performed on him. He became known as "The Man Who Broke the Bat" when he broke Batman's spinal cord, forcing Bruce Wayne to give up the Batman persona while he recuperated.
Deacon Blackfire: A religious fanatic who forms an army in the sewers beneath Gotham, largely composed of the homeless. A movie with this villain could make interesting comments upon religion. There could be personality cult followers of Batman used as a counter point.
Upcoming comic based movies surveyed at Wired
the Speculist site noted the problem of maintaining the quality level in Batman sequels which boils down to quality villains who allow for a quality story.