Sam telling Quorra about sunrises in the real world while making references to Quorra's beauty. This moment was beautifully heartwarming, especially since Quorra was always curious about the real world. More subtly, this helped ease her pain of being the last ISO. It also cemented Sam's and Quorra's growing love for each other.
Sam showing Quorra the real world after escaping the digital world, starting with a Cue the Sun moment.
What's particularly nice about this is that it's not played like a typical romance sub-plot at all. They're clearly enamored with each other, but the attraction is expressed subtly with emotion instead of physicality. The romance is actually separate from the Fanservice.
It's also a Fridge Brilliance contrast to the ending of the first movie. While the first movie ended with a shot of a lit-up, nighttime cityscape, depicting that we are Not So Different from the computer world, the shot of Sam and Quorra taking the bike and seeing a sunrise far from the city and electronics showed that we are different, after all.
A smaller one, but Sam making Alan the new chairman of the board, after Alan's spent the past 20 years trying to look after ENCOM for Sam since Kevin disappeared. Alan seemed to be the black sheep of the board at the start of the film, in addition to being obviously still grieving over Kevin's absence, so it was nice to see something positive happen for him.
Sam reminding Kevin about how they promised that they would play on the same team.
In its own way, Kevin hugging Clu as he derezzes and reintegrates into his body. Sam is one son of Kevin, while Clu is the other, so the parallels are striking, especially in light of Kevin's apology and unspoken forgiveness toward Clu and the mistakes that he, Kevin, had made in creating him. It's a powerful moment that, like the truly greatest ones, is told through simple gesture and body language.
Not just that. Kevin is giving up everything he'd worked for in his time imprisoned on the grid, even his Zen, man. Everything.
When Sam tells Quorra, "Made it," when they get to the bridge after she said they wouldn't make it (a Call-Back to the conversation they had when they first met, with the lines reversed), the normally stoic Quorra grins widely for the first time.
In his own twisted way Clu seemed genuinely happy to see Sam when he first meets Sam. Since he was created by Flynn it sorta gives this troper the impression that it's two rivaling brothers meeting for the first time, happy to see each other first then go back to killingeach other.
In the Flynn Lives ARG that promoted the film, Alan spends a lot of time talking very warmly about Flynn, and constantly mentions how much he misses him. In fact, he even gets a little choked up remembering Flynn, such as in this IGN interview or this live press conference. Considering how reluctant he was to help Flynn in the first film, it's sweet to see how close they eventually became.