At the very end of the game, when Krile lays flowers at the place where Galuf died, feeling sad and lonely, and is immediately joined by the other three party members.
Faris' and Lenna's sister-bonding in the game, but one moment was where Princess Sarisa, on a break from her lessons, tucks baby Lenna in bed, and she tells her about how their father is going to take her flying on the dragon tomorrow. Pan to the next room, where Sarisa's tutor Jenica is wondering why she's taking so long. The scene cuts back to the sisters' rooms, where Sarisa pushed her bed next to Lenna's, and they've both fallen asleep.
Syldra and Hiryuu being resurrected as Summons was immensely touching, especially given how tragic the former's death was.
Gilgamesh's final speech before his Heroic Sacrifice. "Krile, your grandfather was a strong guy wasn't he? Lenna, never lose your kindness towards all life. Faris, try to act like a woman once in a while, if you still remember how. Bartz, I wanted to fight you one last time. Mano-a-mano. You have admirable companions. I envy you."