I am going to jump on the bandwagon and say most definitely Water Temples. In every single game they have not been fun.
Every time I play through Majora's Mask, I usually quit for like a month just because I don't want to do the Great Bay temple. Even though Majora's Mask is my favorite Zelda title, that temple is, in my opinion, the worst in the entire series as a whole. It's a lot more confusing than it needs to be, and the boss is pretty difficult in all honesty. There's a LOT of backtracking, and moving through rooms at slow paces. Sometimes the current of the water will send you into a room you didn't want to go to, and you have to waste a few minutes finding your way back to the main room, which really is a hassle.
As for the OoT water temple, I'm going to say that it isn't THAT bad. The only part that took me a while on my initial playthrough was finding that last key you need. It seemed that I already explored every single room in the dungeon, and yet, I needed another key. It was very time consuming! Also, the biggest problem, and probably one of the biggest flukes in the whole series, is the tediousness of putting on, and taking off the iron boots. You had to do it VERY often, and it takes a lot longer than it needs to. I don't see why the boots couldn't have just been an item like any other, but oh well, I suppose that problem was fixed in the more recent Ocarina of Time: 3D.
Everything was a water temple in wind waker
In Twilight Princess, there's not much to say. The temple was barren of enemies, but it was REALLY big, so it was just a long boring walk.
EDIT: OH GOSH I MESSED UP! I thought it said "Not want" instead of "Now want". Oops >.> Uhh..... I guess I want to have a fire temple. Those are always fun.