Old School: A lot of the bosses in Final Fantasy 2 were hard, then again, I wasn't very old when I played it, it was the first RPG I beat though
Which I guess would make the last boss in Dragon Warrior the hardest since I never beat him at all
Then again, I never got past the part in Final Fantasy 1 where you had to fight like 6 pirates >.>;;
The second to last boss in Grandia 2 was pretty rough for me too, what made it annoying is that everyone kept telling me how easy the last boss was, and I thought thats where I was stuck at. After I killed him, I realized the game wasn't over, and kicked the crap out of the actual last boss
Much more recently Pollux in PSO Ep 3 was a major pain. Castor has nothing on her!