Great question. Tough answer, but I feel pretty strongly on this one.
I chose Skyward Sword and there a few reasons for this, for one I think that the music is beautiful. Yes it's not all that catchy or memorable (to some at least) but it really is beautiful music and it's actually pretty well put together with so much of it being orchestrated.
The big thing about Skyward Sword's soundtrack that puts it as the best far and away of all the other sound tracks, is that no other game utilizes it's soundtrack like Skyward Sword did. What I mean by that is no other game's music effectively draws you into it's area or scene, other then a few isolated cases which I will touch on later. But in Skyward Sword, the music for each area or place fits perfectly for it's place in the game and helps create the feeling that Link would be feeling at that point in time. For a few examples, Faron Woods is great because it's early in the game when you arrive and Link has just more or less got his bearings in a strange new land and is finally striking off into an uncertain world to find Zelda. There's a sense of both curiosity and hesitation within the song that is pretty easy to pick up on when you pay attention whilst playing through the area. Link's only recently gotten to the surface but he's sorta getting steady about it, he spoke with Impa and now he's got a direction.
Another great example, and this song is my favorite in the series for this very reason, does such a great job of helping you feel the area in which it's played. It connects the player to Link and to the world through that. Lanayru Harbor's theme, has a sense of airy emptiness, sadness and regret to it that fits it's theme so perfectly it gives me goose bumps just thinking of it. The area itself is a little sad. There's the story with the Skipper and his lost crew, and the feeling that the Lanayru area as a whole, is a shell of what it once was. So much is missing and this song does an incredible job of expressing that.
Those are two examples, but by in large every job in the game helps make you feel more connected to the world.
That being said, obviously there are many memorable and catchy tracks throughout the series (OoT's Gerudo Valley, WW's Dragon Roost Island, OoT's Lost Woods etc.) all these songs are great and I love them to death but none of them really do much more then make for a good song. They don't really contribute to the world's atmosphere and since Skyward Sword, I need my music in Zelda to draw me deeper into the game. I would say that there are a few songs in MM that do a good job of what SS's soundtrack does (namely Stone Tower Temple and Ikana Valley) but SS is the only game I feel really does a good job of making sure most of it's songs are very area appropriate, rather then just being a memorable song that get's placed number one on everyones top ten favorite Zelda song youtube lists.