Christopher Nolan has finally emerged from his post-TDK relaxation period, albeit only to say that he's jotting down some ideas, and that's as far as any planning has got thus far. However, I'm yet to witter about sequel potential yet here, and with the DVD release of TDK it's on my mind, specifically the potential bad guys, because with that comes a plot, in part at least. Given the "real" nature of the Nolan Gotham, it limits the scope to a degree (for the better, one might argue), to the extent that even the Riddler might be a little bit too offbeat. Plus I can't help but think there'd be a degree of overlap with the Joker in terms of style. Catwoman's another obvious candidate, who would fit into the world well, plus provide potential love interest for Bruce/Batman - unnecessary, I'd say, but it's the kind of thing that makes studios happy. The Penguin has his fans too, and as a business rival for Wayne it could work, if the theatrics were toned down somewhat. However, the problem with all of these is that they've been done before in the franchise, albeit pre-reboot. Clearly we've seen that Two-Face was handled effectively, but at the same time he only featured towards the end of TDK, rather than being a full-blown presence throughout the film.
Two other candidates recently voted for in a fan survey were Bane (not the appalling "Batman and Robin" version, but the comic version, who was a pumped-up brute but intellectual too) or Harley Quinn, on-again/off-again girlfriend, of sorts, of the Joker. I don't see Bane working (although the "Broken Bat" angle might one day make a good movie), but Harley could work, given that the Joker probably won't feature in the next movie, at least, but her presence would tie the two together. If nothing else she might provide a handy support act. However, none of those really swing it for me though - even Catwoman, while she'd fit into the world and bring something interesting to the table, I don't think she could provide a full plot by herself, at least not something with the depth we're now expecting. Then again given her illicit activities and Batman's current fugitive status, an enforced partnership might be a decent development.
In terms of less known and more modern villains though, I reckon there's potential - starting Zsasz, who's a knife-wielding serial killer, seen briefly in Batman Begins during the Arkham breakout (the guy with scars visible on his neck - he cuts himself for each victim, and they cover his body). He may be better as a henchman to a higher-level bad guy, but he's realistic and disturbing, so could fit well. There's also The Phantasm, from the animated Batman film from years back - not sure if she made it into the comics or not. It's a persona adopted by an ex of Bruce's, who masks up in order to kill bad guys. Having good intentions, in fact similar to Bruce's, but with directly conflicting methods, could make for an interesting basis. In the animated film there's also the mystery of who the Phantasm is (I realise I've ruined that now, but it came out 15 years ago, so you've had enough time to see it) - given a reasonable number of fans will know the connection between the woman and the Phantasm it's relatively unlikely that the mystery element would remain, but I still like the idea. Of course that also means that a TDK sequel could end up being a remake of an animated movie, so perhaps not.
Black Mask is another decent psychopath with mob connections - again, similar to the Joker but more organised, and with a backstory that wouldn't necessarily detract from the character's intruge. Also Hush - a childhood friend of Bruce who developed an irrational (well, mostly) hatred of him. After time away he returns to Gotham, finds out Batman's true identity, then recruits a large collection of bad guys to try and destroy him. While the full employment of the Batman rogues gallery is unlikely, the core principle could still work, especially factoring in Bruce's current "on the run" status and feeling in need of a friend, who he then discovers is plotting against him.
My personal favourite thus far though is Deadshot - possibly because I've just watched the "Gotham Knight" collection of Batman animations, and he features in the last installment, which was my first discovery of the character. Deadshot first appeared to be a new vigilante, before turning out to be an assassin who prides himself on always completing a job. I think that gives decent scope plot-wise - with Batman out of favour, a new crimefighter appears on the scene, with an alter-ego similar to Bruce. Batman starts investigating and discovers the truth, then by demonstrating what's going on to the public he proves himself to be a good guy once again. You never know, things could even work out such that Deadshot ends up being blamed for the deaths in TDK for which Batman took responsibility. Just a thought...