The optional Agrabah boss in Kingdom Hearts 1 comes to mind. It took me over an hour to kill that thing. The Phantom was also difficult due to the Instant Death curse it places on each of your team members and I was annoyed that you're forced to have Peter Pan in your party to do the boss battle. I've always hated him, even in his own movie as a kid.
Other difficult bosses I've fought are Primal Dialga in Mystery Dungeon, Cynthia in Platinum on my first run through, Wham Bam Jewel in Hero to Helper in Kirby Super Star Ultra, Galacta Knight from Kirby Super Star Ultra True Arena, that robot worm thing in Shantae and the Pirate's Curse, and Ganon in LOZ Oracle games after defeating Twin Rova when I have no more Magic Medicine to replenish health after all my hearts are gone.