Well, this can certainly be a difficult thing to answer, particularly for people like me who can be a bit indecisive about such things. But I have to say, I believe that Spirit Tracks would have had my favorite soundtrack overall. I recall that all the while through my first play through of the game, I kept stopping just to turn up the volume and experience that music for a few minutes before continuing on. To be honest, that happens with others, too, I just recall doing it more often with Spirit Tracks. I just quite simply... love it. It has a tendency to make its way into my head when I'm doing tasks around the house and such, too.
It's just that the thing is, so much Zelda music is so good, and so different
while all feeling distinctly "Zelda". They all have their own identities formed through their music, and it can be hard to choose one over the other. I suppose the Spirit Tracks soundtrack just sticks out more strongly as a whole than others do in my mind. However, the more I think about it, I do believe that Skyward Sword is creeping up on me now, in this area. It had such a seriously grand and sort of expansive, large feel to it. Honestly I just love them all!