When Ram finds out that Flynn is a user just before he derezzes, finally knowing that the users have not abandoned their followers and that there is hope for the system after all.
When Tron discovers Yori, a shell of her former self and unable to recognize him. He grabs her, transfers some power into her, and she snaps out of it, hugging him with relief.
The cut scene where Yori brings Tron back to her home. She shows him that she still has a playful and rebellious streak (like her User counterpart, who essentially splits the difference between the overly-serious Alan and the less-than-serious Flynn), turning the barren apartment into a beautiful paradise for him and then taking the time to... interface.
The I/O Tower. You hear of Programs speaking of the Users like we speak of Gods, but when Tron finally steps into the I/O beam and connects with Alan, the sheer joy on Tron's face truly delivers how important and powerful the need for Programs to contact their users is.
Gibbs is the stand-in for every single computer pioneer who ever lived (a late middle-aged man in 1982) who still has the streak of rebellion and vision.
When Flynn explains to Tron and Yori that Users are just as fallible as Programs. While disbelieving at first, Tron seems to take the revelation in stride. Perhaps because he now knows both group have something in common.
Tron: If you are a User, then everything you've done has been according to a plan.
Flynn: You wish. You guys know what it's like... you just keep doin' what it looks like you're supposed to be doin', no matter how crazy it seems.
Tron: That's the way it is for programs, yes.
Flynn: I hate to disappoint ya, pal, but most of the time, that's the way it is for Users, too.
Tron: (more amazed than disappointed) Stranger and stranger.
The ending scene. Alan and Lora are waiting on the rooftop helicopter pad for "the boss." Copter lands, and Flynn rushes out, gives his pals a hug, and off they go. The last shot is the Los Angeles skyline fading from daylight to nighttime. The dark sky, bright lights, and neon make the human world look almost indistinguishable from cyberspace, silently saying human and Program are Not So Different.