Demon's Souls.....period.
Ummm, Trema in FFX-2. I had to grind to level 99, then find out from trial and error just what the perfect dressphere combination and techniques to use. Even then, that fight took like an hour or something along those line. I would say Paragon, but if you have the right strategy, you can beat him in like 5 minutes
Sephiroth from Kingdom Hearts 1. I mean, wtf? You first meet him when you're like level 49 or 50. Then he proceeds to whoops your ass in like 1.5 hits. So I grind to like level 65 or 70 thinking I'd beat him. Nope, same thing happened. Level 80? Nope. Only when I was level 99 and had the Ultima Weapon, did I beat him