Greg Cox. The man who adapted 52 and Infinite Crisis from comic series into prose, for the benefit of those with a picture phobia, text philia or completist's streak.
Cox also wrote the novelisation of Rises, an excerpt of which made its way onto the IMDB forums and Nuke the Fridge. In this little throw away reference, Cox starts a rumour about where The Joker has got to.
Here's the clipping:
Now that the Dent Act had made it all but impossible for the city's criminals to cop an insanity plea, it (Blackgate Prison) had replaced Arkham Asylum as a preferred location for imprisoning both convicted and suspected felons. The worst of the worst were sent here, except for the Joker, who, rumor had it, was locked away as Arkham's sole remaining inmate. Or perhaps he had escaped. Nobody was really sure. Not even Selina
Not. Even. Selina.
I guess that, in the novel, Selina is some sort of incredible know it all, totally specced-up on everything about every move of every criminal. She didn't quite come off that way to me in the film… maybe it was the intention. Or maybe it's just that she was in Blackgate Prison for a while and it's assumed she'd know all about the goings on therein.
I dare say it would all make sense if I had more than a few sentences to go on. But then again I could have said that about a clipping from the screenplay and, well, I think we can at least agree there were a few plot holes and baffling bits.
Anyway, that's where The Joker might have been, at least in the novel. As for the film, it's moot. He wasn't anywhere. He's not mentioned, he's off the table. Not really any point speculating.