I voted Zelda, but oddly enough it wasn't for the Water Temple. As a child, I despised that level with every fiber of my being, and still hate it a little, but once I was playing in front of my little cousins, saying this was gonna be hard, and I beat the thing in one sitting. I had memorized the whole thing, with a few exceptions. Now, I may hate it, but I have a grudging respect for the designers for making such a challenge.
The reason I voted for Zelda was becuase, as someone before me mentioned, all the water levels tend to be the most annoying. From Link to The Past to Twilight Princess , but the real clincher for me was Majora's Mask. It wasn't as hard as the Water Temple the first time through, but it was certianly more annoying. So I vote for Zelda the same reason the people who vote Sonic vote Sonic; not for one level, but the series' record with water levels as a whole.