In an interview with MTV News, Michael Caine (who portrays Alfred and is under contract for a third installment of Christopher Nolan's Batman series) claims that both the Riddler and the Penguin will appear in the next film, portrayed by Johnny Depp and Philip Seymour Hoffman, respectively. Hoffman has denied discussing an offer to appear in the movie and claims he might not be interested even if approached for the role. (Read the article here.)
With no villains confirmed to be appearing in a third film, here is a list of possible antagonists:
Two-Face. It was widely believed that Two-Face would be the villain of the third installment. David Goyer, who penned Batman Begins and helped on The Dark Knight, had said that the Joker would disfigure Harvey Dent, aka Two-Face, in the third film. But we now know that Dent is disfigured and becomes Two-Face in Dark Knight. And, of course, he dies at the end. (There is speculation on how and why he might still be alive: see this FAQ entry. And see this FAQ entry on why his return seems unlikely.)
The Joker. Asked about whether the Joker would appear again (which would require the role to be recast), Christopher Nolan said, "I don't know. I honestly have not taken a moment away from what is going on with the film now to even think about that. I don't know. I simply don't know." (See: MovieWeb.com.)
Ra's Al Ghul. Ducard, whom we discover is actually Ra's Al Ghul in Batman Begins, is killed in the train crash at the end of the film. Ra's Al Ghul is an immortal in the comic books. While Nolan's series seems to shun the supernatural, there's no reason that a new villain, believing himself to be the reincarnation of Ra's Al Ghul, couldn't arrive on the scene. Another possibility is that "Ra's Al Ghul" could merely be a title bestowed upon the leader of the League of Shadows, rather than the character's actual name.
The Riddler. In an interview with Movie Hole, Gary Oldman said, "Maybe we don't need the Joker. Because we'll have the Riddler." There has been speculation on the web that one of three existing characters might become the Riddler: Coleman Reese (or Mister Reese - "Mysteries" - played by Joshua Harto); Mike Engel (played by Anthony Michael Hall); or the unnamed bank manager (played by William Fichtner) at the beginning of the movie. None of these characters has the traditional origin or characteristics of the comic books' Riddler, whose real name is Edward Nigma (E. Nigma). Rumors of potential stars to play the character include: Johnny Depp; Michael C. Hall of Six Feet Under and Dexter; Phillip Seymour Hoffman, and Eddie Murphy.On the debit side: the Riddler appeared in the earlier series. (But then so did the Joker and Two-Face.) Trivia note: In one of the newspapers released with the viral marketing, there is a letter to the editor that is authored by Edward Nashton, a common alias of the Riddler.
The Scarecrow. Some fans were disappointed about the Scarecrow's small role in the film. But he does survive the movie, which means he could return with a larger role in the third film.
The Penguin. Despite the Penguin being in the core group of Batman's rogue's gallery, David Goyer has stated, as quoted on Digital Spy, that with the multitude of eligible villains available from Batman's 70 years of publication, he fails to see why characters like the Penguin or Catwoman should necessarily be chosen for potential sequels. Christopher Nolan believes the Penguin to be too difficult a villain to portray in the realistic Batman universe they're trying to create.
Catwoman. In The Dark Knight, Lucius Fox and Batman discuss the new Bat-suit. Batman makes a comment about the strength of the suit, asking if it would be able to protect him from large dogs. Lucius says it should protect him from "cats"-- a possible reference to Catwoman. Note that in Batman Begins, Bruce Wayne, pretending to be drunk, refers to all his guests as "two-faced phonies." At the end of the film, Batman is given the Joker card. That means that both the main villains used in the sequel were referenced in the first film. (See the Penguin entry above about David Goyer's reluctance to use Catwoman in this series.)
The Black Mask. David Goyer has expressed a desire to use a villain that has not received previous film treatment (source: Digital Spy). The news has put Roman Sionis/The Black Mask on the list of possibilities. Fans have noticed that the prisoner on the boat played by Tommy Lister has a tattoo on his neck with the design and pattern of the Black Mask.
Talia Al Ghul. The daughter of Ra's Al Ghul could seek revenge on Batman for killing her father or perhaps try and carry out his plan for destroying Gotham. (In the comics, she is depicted as more of an antihero than an actual villain and also as a love interest for Batman.)
The Mad Hatter. There has been online speculation that Jervis Tetch (alias the Mad Hatter) makes a brief appearance in The Dark Knight, though this name is never used in the movie or in the credits. David Dastmalchian, who is supposedly playing Tetch, is simply billed as "Joker's thug." A look at David Dastmalchian's photo on IMDb will reveal that he plays Thomas Schiff, who is indeed one of the Joker's thugs, one of the "honor guard" who is shot in the confusion following the Joker's attempt on the mayor's life and subsequently interrogated by Harvey Dent. Batman, in stopping Dent, identifies Schiff as a former Arkham inmate.
The Calculator. During Rachel's interrogation of Lau, he makes numerous references to his "calculations being accurate." These references remind fans of a DC villain that originated in early Batman runs known as the Calculator, who began as a campy low-level villain (complete with an over-the-top outfit), only to ditch the costume and lurk behind the scenes. In recent years, and in pivotal DC storylines, the Calculator is an integral part of the criminal underworld, particularly involved in financing criminals and providing information to the world's supervillains. (Of course, if the Calculator does appear, he won't be Lau, who is burned alive on a pile of money.)
Harley Quinn. She is the psychiatrist who works at Arkham Asylum and tries to treat the Joker; but she winds up falling in love with him and becoming his girlfriend/sidekick. But even if the Joker returns (played by a different actor), she is still not a strong contender.
Poison Ivy. She has a number of superpowers related to plants and the environment. In some incarnations, she is more plant than human. But her origin and abilities can always be altered to make her more realistic. In the 90s cartoon, for instance, she was a biochemist who became an eco-terrorist. On the debit side: She has already appeared in the previous series.
Mr. Freeze. His identity revolves around the cold. He has a variety of sci-fi devices that allow him to freeze people, buildings and cities in blocks of ice. On the debit side: The character would be difficult to make realistic. He has already appeared in the previous series.
Great White Shark. A ruthless financier earned the nickname, the Great White Shark before frostbite, and injuries received by inmates at Arkham Asylum, deformed him to the point where he almost resembled a shark. Has never appeared in a Batman movie or TV series.
Sal Maroni. It is believed that if Dent survived the car wreck in The Dark Knight, then Maroni could have as well, even though Dent put on his seat belt and Maroni was not wearing his.
Bane. In the comics, Bane is a highly intelligent, incredibly strong criminal mastermind. He, along with three accomplices, releases Arkham's inmates. Bane breaks Batman's back and takes control of the city. The whole scenario matches the realistic tone of Nolan's series. Although his superhuman strength may be too unrealistic, perhaps his "venom" formula could be re-imagined as some form of steroid.
Killer Croc. In the comic books, Killer Croc, alias Waylon Jones, is a former circus freak born with a rare skin disease that gives him the appearance of reptilian scales. With a few adjustments, he may be plausible enough to appear in this series, especially if the filmmakers to concentrate on his earlier comic book appearances, rather than his more recent re-designs, which go as far as giving him a tail and amphibian abilities. Killer Croc does appear in the animated Dark Knight prequel Batman: Gotham Knight as an ex-patient of Dr. Crane (who was treating his fear of bats) now living in Gotham's sewers. Gotham Knight coincides with the movie universe i.e., The Dark Knight and Batman Begins, which may also affect considerations for his use in any future films in this canon.
Clayface. His ability to shape-shift may make him too unrealistic for this series. Note, however, that several Batman villains have used the name Clayface. The first Clayface was a B-movie actor who assumed the identity of the villain he portrayed in films.
Anarky. The master of social destruction, an ideologist on chaos, a simple 13-old boy. The character's youth could be seen as a gimmick or as an original idea.
Man-Bat. Half man, half bat. This unrealistic creature is a long-shot.
Cornelius Stirk. A psychic who creates fear in his victims. He may be too similar to the Scarecrow.
The Ventriloquist. Commits his crimes via a dummy. He is accompanied by his bodyguard, Rhino. It wouldn't be difficult to rework the Ventriloquist as a believable character. It could be hinted that the puppet has sentience while allowing skeptical viewers to believe the masterly work of the puppeteer is responsible for the illusion of life. On the credit side: Never been in a Batman movie. Psychologically disturbed. On the debit side: Insane ventriloquists are an old theme in movies. See this FAQ entry.
Hush. Could serve as an effective "dark mirror" for Bruce Wayne/Batman, but could also be dismissed as a gimmick villain.
Deadshot. In the comics, Deadshot is described as being the second-greatest assassin in the DC universe (the first being the Teen Titans' archnemesis Slade Wilson/Deathstroke). He previously appeared in the final segment of Gotham Knight, so at the very least, he does exist in "film continuity."
Dr. Hugo Strange. Professor Strange is perhaps the oldest member of Batman's rogue's gallery; he even predates the Joker. Initially depicted as a mad scientist, he later became a corrupt psychopharmacologist who discovers Batman's identity. Keep in mind that Scarecrow is very similar to this character in Batman Begins, as he is a corrupt psychiatrist whose main specialty is psychopharmacology.
Tally Man. Actually the name of two villains, both of whom work as "debt collectors" for the Gotham Mafia. The first was a white man, dressed like a Medieval tax collector. The second, a black man wearing a business suit. They are relatively realistic characters.
Firefly. The Firefly's tendency toward pyromania and gadgets makes him a fairly realistic character and a possibility.
The Reaper - A masked villain with scythe-shaped weapons. He was changed to the less violent Phantasm in the animated Batman: Mask of the Phantasm (1993).