I hate this question, there are so many good boss battles, like the battle with Sephiroth at the end of FF7. The Fights with Gilgamesh in FF5. The final battle with Kefka in FF6. The battle with all of the Judges in FF12 international. The fight against Algus in Final Fantasy Tactics. Jesus, there are so many more…
Final Fantasy is filled to the brim with amazing boss fights. But when it comes down to it…none were more memorable than the fight against Jenova after Aerith’s death in FF7. I mean, it’s not my favorite boss battle- but it’s certainly the most memorable fight for me, I remember how many times I’ve seen Aerith die, because I lost that fight so many time on my first play through of the game- and all my playthroughs of the game itself- afterwards.
But- my favorite fight? That’s not even close to easy. I think, the Proud Clod, and the fight with Hojo, if counted as a single fight, because it’s just outright enjoyable fight with Proud Clod, and the final confrontation with Hojo. Sooo yeah. :)