And the ENTIRE Water Temple in Ocarina of time is in itself an exercise of the hubris that none of us will forget. That is a deserving choice because of the final matchup, Morpha, one of the toughest bosses in the game (although Bongo Bongo gets the distinction in my mind as THE toughest) and a satisfying ending to a great dungeon.
It was an exercise in annoyance, because the speed got slowed down so much thanks to having to go into the menu to change boots, then slowly float down, then slowly walk around until you find that part where you lower all the water with the ocarina, and then you walk around some more and end up eventually filling the water all the way again before finally realising what you forgot to do, so you need to go through all those motions once again. Joy... not.
And Morpha was a total pushover. At least, that's what I think about any boss I end up killing without being damaged at all on the first attempt. At least Bongo Bongo needed some swift work with the bow so as to not getting pushed off the drum platform and having to start over.
Good, hard bosses... Penance in FF X: International Version. Short story: He makes Nemesis (same game) seem like a wuss in comparison. It takes over an hour to defeat him, you need every stat maxed (including even Luck) and even then, you need to do it almost perfectly, or die.
Last set of bosses in Kingdom Hearts 2. Maybe not the hardest battles, but I did get a bit surprised at how tough they were, and how I needed to pay attention. Plus, they were pretty cool. Then again, thanks to the action button, most boss battles in KH2 was enjoyable, even those that were easy.
The last battle in Zelda: Wind Waker. It's Ganon, and he's really pissed, and he's not doing some energy ball trick, but going straight for you. What's not to like?
