The Good ending, where Tidus is given a real human life and appears in Besaid's ocean. The Celsius lands there; Yuna jumps out, runs over to Tidus, and they embrace.
Shuyin and Lenne finally reuniting in death.
The whole point of the game: Yuna trying to find Tidus, spurred by hopes that he is still alive somewhere.
In the middle of the Gullwings charging for helping people out in Chapter 3, the Djose Temple is being attacked, and although they said they had it under control, it's getting worse and the others are all reluctant to help out. Rikku, knowing Gippal is probably there, snaps "I'll pay you myself!" and orders Brother to fly them there.
In Besaid in Chapter 5, Yuna receives a sphere from Chappu made on the day he left. Later on, Wakka names his baby Vidina, which is Al Bhed for 'future'. It shows Wakka is now more confident to be a father, and it's Fridge Brilliance when you realize that this shows just how far he has abandoned his old prejudice and hatred of the Al Bhed.
Paine's sphere where she, Gippal, Nooj, and Baralai talk about what they'll do once their time in the Crimson Squad is over. It's when you realize that Paine is indeed doing what she said she would for them.
The very last scene of the Normal ending, with YRP riding on the deck of the Celsius up into the sky.