When it's a question of which game has the best soundtrack, Skyward Sword wins for me every time. The orchestration alone puts it in first place automatically, but that isn't the only reason I love the soundtrack.
If I were to analyse the entire 6 1/2 hour soundtrack, I'd be here for a very long time; so, I'll make it brief.
This soundtrack is powerful. From the very grand Sky Theme, to the ever so beautiful Fi's Gratitude, the soundtrack is very diverse despite being completely orchestrated. The instrumentation is amazing. I could hang out in the Sky and listening to the beautiful strings and horns with great snaredrum backing for hours. Every single track fills me with a type of emotion that I have never gotten from any other soundtrack in the series. I can't really explain it though, since I am not too sure what that emotion is myself. I just know that the tracks make me happy and sad at the same time, sad because the songs are all so grand and beautiful.
The songs were also very well composed. As much as I love Koji Kondo, I need to give a massive shoutout to Super Mario Galaxy Composer Mahito Yakota for orchestrating such an amazing video game OST. Each song corresponds perfectly to the cutscene/area in which it is represented, creating the perfect atmosphere in each instance the songs are played. Skyloft is peaceful, so it has peaceful music; The Sky is very large and open, so its corresponding audio track is very grand; The Silent Realms are silent and rather spooky, and their respective tracks contribute greatly towards their undeniable eeriness. I was amazed when I first played the game that they were able to compose a soundtrack that sets the mood for literally every cutscene and area in the game. None of the other soundtracks have really accomplished that.
I honestly fail to find much of the music in Skyward Sword to be particularly catchy. Is that a problem though? No. The soundtrack is too well put together to worry about such small details as catchiness. It is primarily the style, instrumentation, and complexity that draws me into a soundtrack, and Skyward Sword accomplishes all of those things plus some.
When talking about soundtracks though, I suppose I should give an honourable mention to that of The Wind Waker. To be quite honest, if it weren't for the excessive use of MIDI to create the tracks, this soundtrack may have won for me in place of Skyward Sword. It fails to fill me with the same emotion that I get from the Skyward Sword soundtrack, but the style, instrumentation, and complexity are all there. The only real problem with it is that the MIDI oriented instruments do not even compare to live recordings. A notable track from this game would be the Ganondorf Battle Theme. The song features a rather complex time signature, and sets the mood for my favourite final boss fight very well.