OoT Ganondorf. I know it's a remix of the one from ALttP, but I played OoT first. It was the coolest thing I've ever heard when I was seven, and when we used to download music, I'd search Napster frantically for it.
I also love the boss theme from OoT and the miniboss theme from MM.
MM regular boss theme! I love it! The MM boss theme and miniboss theme are candy for my ears! The only things that were better with Majora's Mask than Ocarina of Time were the boss themes!
(I'm still trying hard to enjoy Majora's Mask though........ Sometimes it's more enjoyable than other times......)
My favourite theme for any of the Zelda games ever would have to be Ganon's theme, when you're climbing the tower in OOT and he's playing his pipe organ. I'm a pipe organ lover so of course that's my favourite!
The MM regular boss theme is the best boss music, bar none. I can't even explain why I like it, I just do. There's something about the way it sounds that says to me "You're fighting this giant monster and might die." Although I love nearly all of the Zelda music, this one is definitely in my list of top favorites.
I like A Link to the Past's Ganon theme, Ocarina of Time's Ganon theme (love the dark sound to it) and though it may not offically be a boss theme, it still plays during the boss theme and that would be the original Legend of Zelda final dungeon theme.
Mom smokes in the car... Jesus is okay with it, but we can't tell Dad.
It was a really tough choice between the Majora's Mask regular boss music and Majora's Wrath music.
The regular boss theme sounds so climactic and powerful and perfectly complements all of the boss battles in the game (except for maybe Twinmold, but it works very well even then). I would absolutely love to see it orchestrated.
Majora's Wrath, on the other hand, takes a theme that (for me at least, after playing the game for three years before beating it) is iconic and remixes it to match Majora's true nature perfectly: a chaotic beast that could kill you just by looking at you if it wanted to, an utterly insane creature with power that is greater than that of the four guardian deities of Termina combined and almost rivals that of the goddesses. It's a mad, sadistic, nearly unbeatable monster that easily dodges your attacks and retaliates so quickly and in rapid succession that Link can't even stand up after being hit. The rapid tempo and distortion of the once slow and calm theme makes that message very apparent.
Well, that's what it meant to me on my first playthrough, anyway (where it used to make me use two fairies; I as eight and had only the Woodfall Great Fairy upgrade and fourteen heart containers). Now, since I'm much older, I find Majora's Wrath to be an utter joke. That theme is still incredible, though. In the end, I still went with the Majora's Wrath theme despite those developments.
Between ALttP's normal boss theme and and OoT's Ganon battle, for me. It seems like they can get away with just playing good music in 2D games, whereas in 3D stuff, it needs to match or the battle won't be complete.
I actually voted for OoT Ganon's music though. It has the immersion they seem strive for and it's something I enjoy listening to.