The "Save Marbule" sidequest definitely counts as well.
Discovering the Frozen Flame in Chronopolis and speaking with Robo is pretty memorable, too — not "awesome" as in "cool", per se, but the imagery, music, and information being conveyed to you at that moment are all pretty awe-inspiring.
Successfully casting the Chrono Cross Element in the final battle with the Time Devourer.
"I have been waiting an eternity...just for this very moment..." And Schala's soul is freed and healed, and Lavos finally melts away. It may have been Guide Dang It, but that is how one defeats a god.