Sora, Donald and Goofy reuniting after over a year of sleeping.
At the end of the game, Riku admits that he's always been jealous of Sora, and then...
Riku: But there is one advantage to being me. Something you could never imitate. Sora: What's that? Riku: Having you as a friend. Sora: Then I've got something you could never imitate too.
The ending of the game. Also, when Sora gets tackled in a hug by Donald and Goofy and Riku catches Mickey and spins him around.
Sora: We're... we're back. Kairi: You're home.
Hell, almost every scene in the ending; Mickey and Minnie reunited, Beast (now human) dancing with Belle, Jack with his ship, Nala and Simba having a child, Ariel married, Leon reading a letter from an old friend, Sora at Destiny Islands finishing off Kairi's drawing.
"Sora will find the answer we're looking for. I know he will. Because he's me." Though it at first sounds odd, and maybe even egotistical, I can't help but smile every time I think of this moment from KHII: Final Mix. Through most of the game (especially with scene additions), Roxas makes it clear that he wants his own identity, that he doesn't want to just be Sora's Nobody. He lashes out at anyone who calls him Sora, and continuously says his heart belongs to him. But now he's accepted the fact that Sora is a part of who he is, but not all he has to be, and that they can learn to coexist without having to give up anything.
Pluto trying to comfort Kairi in the prison cell of the Castle That Never Was.
Mickey and Donald's reunion with Goofy after his Disney Death.
Sora and Kairi hugging.
Tron's goodbye after defeating the MCP.
It's even more Heartwarming in Hindsight. Kingdom Hearts 3D: Dream Drop Distance reveals that programs are somewhat like Nobodies, as they don't have hearts either. The same game confirms that Nobodies can grow their own hearts, given time, and it's quite possible that the same could go with programs. Tron is a program, and thus does not have a heart at first: his friendship with Sora allowed Tron to grow one of his own!
A little tiny one: After Mickey reaches the unconscious DiZ (who, of course, is actually Ansem the Wise) in The World That Never Was, the latter starts to stand up. DiZ stumbles for a moment, then glances at Mickey, who he's using to support himself. He pauses for a moment before standing, which this troper interpreted as giving his old friend a hug.
A rather nice little moment occurs while Santa and Sally are talking. While chatting Maleficent and Oogie Boogie attack them in an attempt to capture Santa. Despite not knowing Sally for more than a few minutes, Santa valiantly puts himself in front of her and their attackers. Pure of heart? That's Santa Claus alright.
If (by some incredible chance) you lose to Setzer in the Roxas prologue, Roxas returns to his friends looking disappointed. The four are silent for a moment. Then Pence starts clapping, followed by Hayner and Olette.
When Donald and Goofy finally get to reunite with Mickey at Hollow Bastion. They'd seen him before at Twilight Town, but this time they actually get to run up and hug him.
The entirety of the reunion between Mickey and Minnie. Dear lord, if anyone deserves a happy, heartfelt reunion that is not interrupted by Heartless, nobody or some other adversary trying to kill them, it is those two... and they get one!
Then, there's the music. It's an upbeat version of Disney Castle's theme that hits the crescendo as we see King and Queen reunited. Then, as they touch, hands to hands, nose to nose, the music settles down into their romantic theme.
Yuffie and Aerith fighting together (albeit somewhat offscreen) during the attack on Radiant Gardens and within the 1,000 Heartless War; when Yuffie collapses from exhaustion, Aerith busts out a Curaga spell to keep her ally going.
We get the scene of Sora allowing Demyx to use his Olympus Stone, despite the objections of his friends.
Also Kairi allowing Demyx to return her to her cell after she escapes because he's practically in tears over what Saix will do to him if he fails. Kairi later tells Riku that she empathized with Demyx and Axel.
When Sora manages to snap Donald and Goofy out of a Heroic BSOD when the trio find themselves trapped inside a computer after being sentenced to death by the Master Control Program, and their only means of escape is accidentally destroyed.
Sora: Don't give up! Don't you remember? When we get out of here, we get to see the King. What's the big deal about parts, anyway? If we can't find one... we can make one!!!!
Upon returning from Timeless River, we see that King Mickey has secretly shown up, ready to help out with saving Disney Castle... only to learn that they already succeeded.