This is a tricky question because there are really two ways to look at it.
First and foremost, Christopher Nolan didn't technically "intend" anything for a third film, because The Dark Knight was written and filmed on its own and without any direct view toward a sequel. Mr. Nolan didn't know if he'd want to ever make another one. It took a lot of convincing by Warner Brothers to get him to come back for the second film anyway, and his attitude is to approach each film as a stand-alone production and not think about what comes next.
Christopher Nolan almost didn't come back to make this third film, remember. He was very close to walking away completely after making The Dark Knight. He returned only because of the long months spent by himself and David Goyer drafting a story that made Mr. Nolan feel compelled to return and make this new film.
So on the one hand, then, Christopher Nolan did not "intend" for the Joker to appear in The Dark Knight Rises because Mr. Nolan didn't have a specific intention to even make a third film at all, and the story for it only developed later.
Now, on the OTHER hand, upon completion of the film, some people close to the production have said that Christopher Nolan's work with Heath Ledger resulted in a close friendship between them and an immense respect and love for what Mr. Ledger did in bringing the Joker to life in the film. From that, there was -- again, according to some people who worked on the film -- a very broad and general sense that IF a third film was made, then whatever else it was about, Heath Ledger would probably be asked to come back and reprise his role as the Joker in some form or fashion.
What form or fashion, nobody knows, because it was just a very general impression of, "If we make another one of these films, we'll probably want that Joker to be part of it somehow." There was no story, no specific role the Joker would play, and not even any certainty or more specific talk of whether there even really would BE a third film.
Some people mistakenly believe there was actually a story or outline for a third film featuring the Joker. What they are talking about, however, is that way before any script or story was written for The Dark Knight, David Goyer had (sometime after Batman Begins) drafted an outline of an idea for two films that would involve the Joker. The first would have been the Joker rampaging in Gotham and being caught, and the second film would have featured Harvey Dent prosecuting the Joker. During the trial in this second film idea, the Joker would throw acid or something in Dent's face, turning him into Two-Face, and thus giving the third film a rampaging Two-Face for a villain.
That was the very rough idea sketched out by David Goyer in the aftermath of Batman Begins. But it was just the basic idea, and parts of it were kept and merged together into one single idea, which became part of the story in The Dark Knight. So the rumor that there was a third film planned with the Joker is just a misunderstanding about the early concepts written by Mr. Goyer for films after Batman Begins, and those concepts all got into The Dark Knight and none were left over for any planned third film whatsoever.
Christopher Nolan wasn't sure he'd ever want to make another Batman film after The Dark Knight, and he had no specific plans to do so. He didn't have a story or an intention to make a third film, so he had no intention or plan for the Joker appearing in any such third film either. But it can probably be said that after working with Heath Ledger, in the time prior to Mr. Ledger's tragic death, Christopher Nolan probably looked at this film he was now putting together and editing and thought, "Wow, if I ever come back for a third film, I hope Heath will come back as well."More questions on Batman: