Some milestones for me:

(SPOILER)Killing Algus was satisfying.

Getting Thunder God Cid in the party. It's like C. Everett Koop that has come to kill you.



Getting all the Nelveska rare treasures and recruiting a Hyudra and keeping Worker 7 alive at the same time.

Breeding my first Tiamat; they're my favorite monsters in the game.

Learning Zodiac.

Teaching Zodiac to my entire party, by lowering enemy humans' faith, hitting them with Zodiac, then picking up the crystals.

Finishing off the Proposition list including all rare treasures and undiscovered lands. I played the game through once to work it all out.

And finally: getting at least one of every item. My completionist impulses were finally rewarded. I've never been able to complete any other game in this way (although I've come closer).