It's so interesting how so many people have such different opinions when it comes to difficult bosses. We all have unique experiences with each game that result in different bosses being the most annoying.

I think I had the most trouble with Seymour Flux in FFX. I also had trouble getting inside Sin, but that's because I was being really stupid. :P

Anyway in FFVII, I didn't have much trouble with any boss, though I remember the battle with Sephiroth's penultimate form taking forever. As for some of the other FFs I've beaten (IV, VI, XII), I sorta kinda cheated. I powerleveled all three of those, so none of the bosses were very hard, though I feel like all three of those games could have been quite difficult had I not powerleveled.

Note: To be fair, I don't think powerleveling helped very much with final bosses -- it just made general gameplay easier.