The way the Goblins set up their trap for Graham in the canyon. The camera is positioned so that the Goblins aren't seen until after Graham passes them by, and suddenly you see the rocks moving...
The battle against the Goblins after that.
The Bravery choice in the prologue against the Dragon in the Well. If you're aware of the Foreshadowing from previous playthroughs, you can practically hear Graham thinking, ''This is forAchaka, you son of a bitch!''
The fact that the game plays with its Karma Meter system. The characters who exemplify each of the three ways are in situations where their favorite way doesn't work, and find themselves forced to try the other ways.
For instance, Wente (who favors compassion) first tries to be kind and give cakes to his captors (compassion/kindness). When it fails, he decides to give them more cakes... POISONED ones (wisdom/intelligence). And when THAT fails, he snaps and just clobbers them with rocks, knocking them out (courage/strength).
The climax for many reasons, especially the fact that it pushes the parallels between young!Graham and Gwendolyn to their highest and best level.
The entire sequence of Graham climbing Hagatha's castle to save the princesses while it's being engulfed in ice. The actual climb is tricky, but the cutscene is worth it.
The introduction to Manannan shows that he means business.
The newly reunited royal family working together to solve the labyrinth. You can really see how much they all care about each other, and they each get to show off their respective strengths.
Doubles as a Heartwarming Moment. After the credits of the epilogue, Gwendolyn is shown standing triumphantly on a cliff facing the sunset (or sunrise?) holding up Taskia's bow as if she's telling Graham that she finished her first adventure.