FF VI - This is likely the boss I've had the most trouble with over the years. It was situational I think, and related a lack of leveling I put into Sabin. But nonetheless I remember dying repeatedly to it, getting annoyed as hell because of the long walk through the cave to get to the boss (no save point near by), and generally having to sit around leveling up a bit. I think I had trouble with at least 3 playthroughs back in the SNES and maybe PS1 days.
I'm not sure if I'd still have trouble today - I'm a much more serious gamer now so perhaps I'd reconize an important Relic or spell that makes the fight easier, or my tendency to level up more would simply make it easier - but nonetheless it's still likely the hardest boss I've had to deal with over the years.
I can't think of any boss I've had trouble with since FF6. From FF to Suikoden, I generally just level up too much. SaGa Frontier perhaps, but only because the difficulty scaling was quite unprecise, and you could find yourself in regions where the game under or over scaled (making the game much too easy or too hard, rather than be precise enough to find the exact suitable difficulty).