First things first, I have to say Skyward Sword's music was simply phenomenal and one of the best soundtracks to ever grace gaming. Easily the best in the series, and without a doubt some of my favorite.
To start the list off, this boss battle track is one of the most energizing and battle-appropriate tracks I've ever heard. It just makes the feeling of "Bring it on!!" scream inside me. Bosses by themselves in SS were great, but their music really sold the feeling the fights were supposed to present, and that's a welcome factor to me.
[video=youtube;MzL4IA16k78]http://www.youtube.com/watch?v=MzL4IA16k78&list=PLC5AE6E1EEA630D30&index=94&feature=plpp_video[/video]
This one isn't my favorite in the game, but it perfectly fits the situation its set in, which is the impressively creepy Guardians Awaken sequence. It's also just a kick-*** track.
[video=youtube;n8_LJN-dxtc]http://www.youtube.com/watch?v=n8_LJN-dxtc[/video]
The Sky's theme is one of the most grand and adventurous tracks I've ever heard in the Zelda series, and it captured the sense of freedom and open space the Sky provided perfectly.
[video=youtube;nRbROTdOgj0]http://www.youtube.com/watch?v=nRbROTdOgj0[/video]
Finally, this last track is possibly my favorite track in the entire series. When I first heard this music, I just stood there with chills down my spine. It fit the atmosphere so well. So desolate. So abandoned. So lifeless. Yet there was obviously life in the past. Never before had a piece of music in Zelda done this to me. I've heard plenty of lovely tracks in the past from the series, but this one just captured the emotion of the area effortlessly, and while I don't think it's necessarily the best track in the series, the impact it had on me earns its title as my favorite track in Skyward Sword.
[video=youtube;0LfAcKnDYWQ]http://www.youtube.com/watch?v=0LfAcKnDYWQ[/video]