I can recall an Ice Temple in Oracle Of Seasons that was ridiculously hard with all those ice blocks to push about.
The Stone Temple in Majoras Mask was just unforgiving
The Fire Temple in Twilight Princess as I recall was a freaking maze of lava and metallic frames.
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Am I missing something? Why does everyone suddenly hate Stone Tower? In my opinion(and I KNOW I'm not alone), it's the best dungeon in the series!
Anyway, fanboyisms aside, I'd have to say the worst dungeon in the series was Jabu-Jabu's Belly from Oracle of Ages. It basically ripped off the Water Temple's defining concept of changing water levels, it contained an upgrade to the game's equivalent of the hookshot, just like the water temple, and it even had a generic blob as a boss. Mind you, I liked Morpha, but this is just unforgivable. It's basically the Water Temple, only several times harder, and even more annoying.