The Hyrule Symphony album is certainly the best versions you can hope for when it comes to Zelda music.
But there is one track in particular from that album that blows me away every time I hear it :
Gerudo Valley.
The original used MIDI guitars with a splanish flavour. This version is done mostly by violins.
And it is awesome. So powerful, so intense, so-mind blowing, you'll never get tired of it.
The surprising thing is that even when you are a hardcore fan, you won't recognize the theme for the first 30 seconds, since the two versions have a completely different feel.
Also, let's mention the Goron theme who is really great in this album, and of course, the Zelda medley, the ultimate track for all the fans.