Gilgamesh is up there, of course.

Trickster was also kinda fun. Chasing a semi-invisible chocobo around, wouldn't have thought I'd be doing that.

Also, I liked how Orthros was an allusion to Ultros, especially with its spawning condition.

Finally, the Belito hunt was great. I didn't pay much attention to the sidestory of the hunter killer, so suddenly seeing Ba'Gamnan was quite a nice surprise.