I love Majora's Mask and in fact it's my favirote Zelda game but every time I play it a just dread the Great Bay Temple. It's not just that it's hard it's just having to go back in forth to change the water flow and always by accendent falling into the water making me go have to go the long way back to the room I was in. Although the Zoras mask was amazing the temple was just plain annoying and also had a bad boss in my opinion.
I hated King Jabu Jabu in Oracle of Ages. I never hated the water temple from Ocarina of Time but all of the problems other people had with it I felt in the OoA jabu jabu. The fact that it's 2D made it more fustrating to change the water level on so many confusing floors.
I hate the City in the Sky. Overall a horrible dungeo in a bad Zelda game. Tedious layout, very boring enemies, lame boss fight, very boring to look at, and okay music. I know almost everyone hates the City in the Sky, but, my goddess, it's bad.
City in the Sky, I didn't like many parts of that, and the partners temples in WW were other ones that annoyed me from time to time... but the main reason I was annoyed with those temples was keep playing the freaking song...
I actually like the Ocean Temple a lot... after going throw it several ( :O ) times... now I can make a run throw that in crazy amounts of time... the phantoms are right there and its like oh no spotted again? oh poo, never get catch though...
Water temples can be very annoying... for example great bay in MM I really didn't like that one... I keep going back and forth back and forth...
But that being said, even though there are parts that really annoyed me... I don't think there is a temple that I out right hated... at least completely... that is...
The only dungeons I hate are the Skyview Temple (SS), Temple of Time (TP), Wind Temple (TWW), and Temple of the Ocean King (PH) (I've only beaten PH once, and it was when I rented it, so I don't remember all the dungeons very well).