zophar from lunar 2. was underleveled and was practically out of items when i fought him, made that battle hell.
and my more comedic one is Gary from pokemon red. Finally taught that punk that i was the true pokemon master...and then did it 70+ more times for good measure and money.
Luca Blight from Genso Suikoden II. No doubt in my mind. You needed to fight him with three separate parties of six and then personally duel him. Even then it wasn't a guaranteed victory. Bad assed, murdering mad man.
Well for me is more kinda a mini boss but hard as hell to kill I even found it more hard than lord saddler (RE4) well my favorite boss well mini boss is the super santo (the double wielding chainsaw guy).