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.