I'll say finding Lix was the most memorable moment for me. My Home, Sweet Home is used perfectly to invoke an atmosphere that feels both homey and lonely. And the way all the villagers talk to Bartz and he doesn't say a single word back... and then you go to sleep and Bartz visits his mom's grave... it was moving.

Honorable mention to Galuf's death and Gilgamesh self-destructing against Necrophobe.