I had a couple bosses that cause quite a problem. Many of them I found cheap ways long after beating them the hard way. Most notable ones I can remember:
The fake Feral Chaos in Dissidia Duodecim. Only being decent with one character, an opponent with three times the amount of HP as your character can have and a lack of skill in Fighting games made this one very long ordeal. I beat him at some point, but needless to say: I never got close to the real Feral Chaos.
Dullahan in Golden Sun TLA. That was before I knew that you could just summon spam him to death. In general I usually play the games without summons so it never really came to my mind abusing that mechanic, so yeah, the fight ended up being somewhat hard and took a couple tries, even with relatively high leveled characters.
Pluto in Tales of Phantasia (GBA): literally the easiest version of him, as you can just spam Demon Fang which not only always hits him, but also prevents him from doing any attack due to stun lock. Didn't know that back then, therefore you can imagine that I got wiped out a couple times. Ultimately I had to resort to coming up with a strategy that forced me to continually switch between characters in order to string their attacks together in such a way that Pluto never got the chance to cast one of his devastating spells. It worked, but just one screwup basically meant losing the fight.
Looking back: having to come up with your own weird strategies for fighting hard bosses because you don't have access to the information the internet provides can be a long-winded and tedious task, but man it certainly is something special if you manage to get it to work.