In my opinion, I actually haven't gotten to the hardest one yet, lol. The easiest one by far was the first dungeon in Phantom Hourglass. My DS broke before I could get to the harder ones, though, so I'm stuck with a half finished game! And MM seems pretty hard to me.
If all pizzas are pies but not all pies are pizzas, then some pies must be pizzas! I'm smart!
The Water Temple by miles... it wasn't just that it was hard, but at the half way point just before you think you're going somewhere you have to go against Dark Link. Thats hard, so of course I couldn't kill him for ages.