Dungeons, Bosses:
Twilight Princess Stallord - It's based on the dinosaur battle music from Ocarina of Time but this one has the advantage that you fight while spinning on the spinner. The fastness of the music along with the sort of time limit in how close you are to the top of the tower go really well together.
Ocarina of Time Forest Temple - Eerie music to go with a dark and spooke temple. Not much else to say.
Wind Waker Phantom Ganon - Again this isn't the first game this music has appeared in but the
Phantom Hourglass final battle - It's catchy, and evil sounding despite it being
Linebeck's theme
Wind Waker Helmaroc King - Not that good to listen to by itself but in the moment it's quite epic. It fits well with how you're contrained to a small circle whereas, being a bird, the Helmaroc King can go anywhere it likes. Plus the spotlights shining on it when it flies away is cool. Not that that has to do with the music.
Twilight Princess Suit of Armour Miniboss
Wind Waker Jalhalla
Overworld, other:
(all of them) The Legend of Zelda theme
(all of them) Great Fairy Fountain, File Select Menu
(all of them) Zelda's Theme
(all of them) Hyrule Castle
most of Wind Waker including
Wind Waker credits
Wind Waker title theme
Wind Waker Hero of Wind
Wind Waker Earth God's Lyric
Wind Waker Wind God's Aria
Wind Waker Legendary Hero - This and the above songs are some of the main reasons I love Wind Waker. This one is such a Zelday tune, it could compete with the main theme for Zeldayest.
Majora's Mask Clock Town - I love how it gets faster every day as their doom grows nearer. It still sounds happy at the same time though, it gets across the denial some of the citizens are going through, or even just Link's bravery. Don't worry, you're all going to die in three days but I won't because I can just reset everything LOL.
Twilight Princess Hyrule Field - This one is so fun, and it changes depending on whether you're fighting or on horseback! Unfortunately the actual field, while beautiful, doesn't instill the desire to explore like most previous games' fields do.
Skyward Sword Ballad of the Goddess