Well Joker can be in Black State Pen. That was a prison in the Batman comics were most of Batman's criminals went too. Super villians and mobsters. So Joker can go their since Arkyum and Narrows gone.
The Joker has already shown that he is smart enough to escape when he's been held captive--from a
police station, no less. Plus, if they sent him to Blackgate it's as good as saying that the justice system considers him sane, in which case they could execute him. Which would suck.
As for the whole, "let's see other villains" idea, I see where people are coming from with that, but at this point I'm much more interested in seeing the conclusion of the story. There are a lot of loose ends to be tied up, and the Joker is one of a handful of people in Gotham that know the truth about what became of Harvey Dent, and what Batman and Gordon are covering up. (Helen Ramirez might be the only other person). I suppose that that, as some have suggested, the Riddler could figure this out and use the information somehow. But, to me, his presence would be a kind of wedge that disconnects the conclusion of
TDK (Batman taking the fall so that the Joker doesn't "win"), from the third movie and Batman's (presumed) redemption. Unless they retroactively tie the Riddler into
TDK, his storyline might feel like a tacked-on addition, rather than a natural continuation.
I just think that the Joker casts too big of a shadow on the story (thus far) to be dropped from its concluding chapter. I want see the other villains in future movies, but not as much as I want to see Nolan finish up what
TDK started.