For me, it'd have to be the Shadow Temple in Ocarina of Time. Not only did I keep on getting lost, I also was creeped out like crazy. Thus the whole temple taking at least a few days to complete.
For me, it'd have to be Volvagia. Not only did I love the "Whack-a-Mole" style, he was also a dragon, and that is enough reason for him to be my favourite boss. In fact, he's my favourite boss of all time.
Also, I felt kind of sad whenever I got to the Volvagia part, after knowing what his role...
I never use my Master Ball. I try to catch all legendaries with Pokéballs, and it has succeeded with about 15 of them! :D
And then I use it on a Bidoof.
I actually really liked both Phantom Hourglass and Spirit Tracks. But I preferred Spirit Tracks more since I loved the train mechanic. And besides, Spirit Tracks was my first ever Legend of Zelda game! :D
A Wind Waker remake would be awesome, but in my opinion, it is not needed as the game is great as it is currently. I think Nintendo are focusing a little too hard on remakes.
The only one I would complain is Inside the Deku Tree and inside Jabu Jabu. The Deku Tree because it really was quite pointless since the Deku Tree gave you the… er…*thing… forgot its name… After you came out of him. Jabu Jabu because it was such a pain of a dungeon, and it was quite lengthy...
I actually didn't like Majora's Mask that much, while I loved Ocarina of Time. Sure, Majora's Mask was a great game, but after a while it just starts to get boring, and the game felt like mostly sidequests. I found the dungeons uninspiring, the bosses weren't as memorable as the ones in Ocarina...
I found the Master Quest WAY too hard. I died three times Inside the Deku Tree for some reason! :P
And one of them was bumping into a gold Skulltula. Boy, was that embarrassing.