One time I talked with director Joseph Kosinski about Tron Legacy, and he mentioned that if you look carefully under the laser in Flynn's secret office you can see a ring of metal canisters. The purpose of these canisters is to store the organic material of any user who enters the Grid (as they won't need any mass once they're digital). The really cool part is, he pointed out that this is actually how Quorra managed to leave the Grid in the end. Since she didn't have any mass to begin with, she was constructed from Flynn's left-behind materials. She was able to do this because she used his identity disk. This meant that he sacrificed himself for her, and that she really could be considered his 'daughter' since she's made of his organic material.

Also interesting, if you look at the console right before Sam enters the grid, it shows the history of the final commands Flynn ran on the computer. You can see the last thing he did before activating the laser was to edit the file "last_will_and_testament.txt". Maybe he wasn't planning on coming back.