I'm probably in the minority who enjoyed the Lakebed Temple in Twilight Princess. Really liked how the entire dungeon itself was a puzzle. I guess the only thing that brought it down was the boss fight; as cool as it was, it was excessively easy.
As far as bosses, I've got a few. That dragon from the sky city in TP, the big robot with the four swords in Skyward Sword, Ganondorf in Wind Waker, Dark Link in Ocarina of Time (yeah yeah, mini-boss but it was still way more memorable than the actual boss), and probably a couple others that I'm forgetting.