The arcade being made at Disneyland's Adventure Park complete with classic 1980 games!
When Sam first lands in the Digital World, complete with the Flynn's Arcade in the background and a Recognizer hovering above him
The entire fight between Sam and Rinzler, but especially when they suddenly find themselves fighting upside-down.
Since Rinzler is really Tron it also adds more guts on Sam's part for facing Rinzler twice and surviving.
The face-off at the End of Line Club. Specifically when Kevin Flynn appears and turns the tide of the battle pretty much by just standing there.
To elaborate further Flynn merely lays a hand on the floor of the club and everything just stops. The lights flicker off, the music comes to a grinding halt, the fighting abruptly stops, everything. Hell, even Castor is left speechless, simply looking upon him in horror.
It is Joseph Kosinski's feature film directorial debut. IT IS HIS FIRST FEATURE FILM. (He had previously only directed commercials). Real Life Moment of Awesome.
And doubles as a Real LifeCall Back; the original movie was Steven Lisberger's feature film directorial debut.
At the end of the "The Next Day" documentary where Sam pushes past the reporters and enters the elevator: one reporter asks if he has any statement for the press. His response is to open his jacket and show them the shirt he's wearing: FLYNN LIVES.
Which is even more awesome and heartwarming if you think of it in terms of Fridge Brilliance - of course FLYNN LIVES - he's Sam FLYNN and is taking up his father's legacy.
Giving Quorra some much-deserved love, this troper loved when she helps Sam take out Rinzler in Clu's quarters despite having her hands cuffed behind her back.
A Real Life example, having the crowd from San Diego Comic-Con be the Disc Wars audience, as seen in the "Disc Roars" feature on the Blu-Ray version.
Though not shown, Quorra's story of how Kevin saved her mentions that she was surrounded by Clu's soldiers, likely including Black Guards. Then Kevin appears over her to rescue her. Though she doesn't say it outright, the implication is that Kevin fought off all of Clu's troops to save her.
The light cycle scene like the first movie was one of the awesome moments. Most specifically the scene where it was just Clu and Sam. Sam was knocked off his cycle and rather than run like hell, he faces Clu head on with his disc drawn. Fortunately help comes Just in Time.
Speaking of Clu, how about his New Era Speech?: "Out there, is a new world! OUT THERE IS OUR VICTORY!!! Out there... is our destiny!"
Also qualifies as a Call Back to Kevin's speech to Encom and, more generally, as a Rousing Speech to his troops. A villainous example, mind you, but that's beside the point.