Tron: Legacy director Joseph Kosinski Gave some solid leads as to where he might take a third Tron film if he is able to:

“I think we will pick with where TRON: LEGACY left off with Quorra in the real world and what does that mean and the possibilities it opens up for the next chapter. It’s that relationship between the two of them that’s the next step.”

He also agreed that the son of Dillinger, played by Cillian Murphy, would have to play a big role:

“Dillinger was a really important part of the first film and felt like an easy way to continue that storyline and thread to have his son in the new movie. That way you have people ask those questions of what the Dillinger legacy is in the world of TRON. We didn’t want to ignore it completely and it leaves a really nice springboard for some intertwining development for the next film.”

via ‘TRON: Legacy’ Director Joseph Kosinski Talks ‘TRON 3? Plot | /Film.

Some of the extra’s on the DVD/Blu-Ray release hint at this these story lines and certainly an area I think would make for good ground to cover for a third film.  Be fun to see it develop.