Eh...let's think about it a different way. I'm going to depart a bit from the ideas that have been thrown around this board and present me own ideas for what could be some good sequels.
First of all, I have to say I'm on the side of the people who say that Joker scarring Harvey Dent would feel too coincidental, too much of a way to connect everything.
Now, I know I'm going to be hanged for this, but what about not scarring Harvey Dent until the middle of the THIRD film? Now calm down...I'm not finished. My reasons for saying this are these: In TDK, we've got Joker killing innocent people and basically being a pain in the neck for Batman. We all know Joker's not going to die, so this story could be about like Christopher Nolan said, "things getting worse before they get better". Think about it: the Joker, Mr Zsaz, and Scarecrow causing havoc (with Joker being the primary and best villain of course). Then, we have the cure for this fear toxin, so they give it to Carmine Falcone in order to try him in court BUT he gets off on some technicality or because of some crooked judges and starts ruling Gotham again through his thugs. This could set up the rivalry between Falcone and the new mob boss Maroni, and it could also introduce Harvey Dent as the district attorney who tries to bring them both down. Meanwhile, Batman's dealing with the maniacal Joker and, done right, that could basically envelop the story of TDK ending with Joker getting shipped off to Arkham(albeit with some cryptic joke, of course) and Batman, Dent, and Gordon on the rooftop(just like the first movie) allying to stop crime in Gotham, leaving some hope for the future.
Now, the third movie focuses on the gangsters. Harvey Dent becomes obsessed with taking down Falcone, while Batman also tries to stop the gangsters from destroying Gotham City. The tagline could even be "I believe in Gotham City." Maroni is finally convicted, but he scars Harvey in court. Harvey goes to the hospital, Batman dealing with Joker escaping from Arkham, Harvey escapes, finds Falcone. Now we could have a stand down with Batman, Joker, Falcone, and Two-Face. Two-Face flips his coin; it lands on the scarred side. He shoots Falcone twice in the head and he escapes. Batman goes to pursue Two-Face, but Joker blocks him and starts lauging manically before saying something like "It's too late, Batman. Gotham belongs to the freaks now. Like him, me...and you." Batman and Joker fight; Batman takes down Joker (something symbolic of Batman conquering his fear) and pursues Two-Face only to find that he's turned himself in saying darkly that "Justice has been done." And, we find Batman standing alone on the building where the first two ended and saying "I believe in justice." "I believe in putting fear...into those who prey on the fearful." Then, we see flashbacks of Batman's father. Batman finally takes his mask off revealing Wayne's face as he looks out over the Gotham City skyline. "I believe in Gotham City." Cue credits.
Now, I think that that would be a good trilogy of Bat-films and I'd like to see what other people think.