There are really too many to list for me. A quick list but I'm sure I'll forget a few...

The opening on the red wings

Cecil and Kain heading to Mist

Mist destroyed and Rydia summoning Titan

Edward seeing Anna's spirit

Kain's Betrayal and Golbez's entrance

Cecil washing up near Mysdia

Cecil becoming a Paladin

The whole Dark Elf Scenario

Any of the battles with the Four Fiends

The battle against Calcebria and Golbez, as well as Rydia's return

Going to the Land of Summons (Feymarch)

Going to the Moon and learning about Cecil and Zemus

The big battle with the Giant of Bab-il and the casts heroic return (screw all of you who wanted them to stay dead, that scene was awesome )

The entire Battle with Zemus/Zeromus, starting with Golbez and FuSoYa fighting Zemus down to using the crystal to give Zeromus physical form.

Really, I felt this game just had too many good scenes.