When little Mayfee's prayers to her "guardian angel" to make the water wheel work are apparently answered and she races off to tell her grandmother. Kalas smiles as he tells the boy who repaired the wheel to come out of hiding.
While on the way to Mira, Kalas asks his Guardian Spirit (you) if you trust Lyude. If you answer yes Lyude smiles and thanks you. It's just a small thing, but still, a very heartwarming moment.
I know most people think of it as a bad case of Narm. But I was always moved by Kalas's apology after he wakes up. I know he was The Mole and all but COME ON! Give the guy a break! I know the whole (deal with Melodia for power) thing was horribly wrong and all but. He literally got on his hands and knees to beg everyone for forgiveness! What more do you want!?
The fact that he's practically in tears as they tell him it's okay really sells it in my opinion.
While the group is camping in the desert, Kalas learns that Savyna was one of the soldiers responsible for the attack that killed his little brother and grandfather. For the rest of the night and well into the next day Kalas apppears to be in a state of shock and doesn't speak to her. Later, while fighting a Fadroh-like monster Savyna is on the ropes Kalas sees this, calls to her and tries to come to her aid. He's prevented from helping but, it's the thought that counts.
Kalas and the others relaxing at the victory banquet. From King Ladekahn and Queen Corellia's sharing thanks. To Kalas suggesting to a despondent Lyude that he should help Alfard in it's efforts to rebuild by becoming it's new leader, telling the nervous young man he's more than qualified at this point. To Savyna taking up cooking thanks to encouragement from him and Mayfee.
Kalas and Xelha reuniting at the end is just golden.
The last scene of the game, when everyone gets together to say goodbye to the Spirit. The characters you've gotten to know give you their heartfelt thanks for getting them through it all. There's something oddly satisfying about it.
If you spared them, the Terrible Trio from earlier pull one Big Damn Heroes after another just to get Sagi and Milly out of the falling Tarazed. Especially so when you hear that Heughes and Nasca are both prepared to sacrifice themselves to save Sagi.
How about the Heart-to-Heart? When you tell Sagi you want to be part of him, he sounds so genuinely happy you can't help but feel for him. A lot of it stems from the excellent writing, which really makes Sagi into a lovable character.
Heughe's letter to his brother Nasca. Considering that by the time you accidentally get it, they've both wiped the floor with your party, it does a good job of humanizing Heughes. Sagi even forwards it to Nasca, despite the fact that Nasca literally shot Sagi in the face with missiles earlier in the game!
Pretty much any time Guillo and Milly express any kind of affection towards the other.