Tower of the Gods - Wind Waker
The scene where the Tower comes out of the sea is frigging epic. The music is amazing, and the boss is pretty cool.
Bottle Grotto - Links Awakening
Nostalgic. Remember spending about a month trying to get the boss key, realising you needed to kill the three enemies in order in the key room. When I finally did it, I literally shat bricks.
Spirit Temple - Ocarina of Time
Loved every second of it. Fighting those armoured knights, getting the Mirror shield and fighting the witches (probably the best Zelda boss made).
Inside Jaba's Belly - Ocarina of Time
Annoying as feck carrying Ruto around everywhere. Falling down the wrong hole is the biggest facepalm in the game.
Temple of Time - Twilight Princess
SO much potential, but having to guide a statue the entire dungeon is really annoying. The control rod sucks.
Snowfall Temple - Majoras Mask
Mostly because it took me longer than Water Temple to figure out. It's an OK temple, but just have bed memories.