Since this thread is back in action, I thought I'd weigh in. Here's my top 5.
1) A Link To The Past - Excellent remix of a classic theme! It screams adventure, and embodies the game's overall spirit. Wonderful through and through. I would consider the Dark World theme a part of ALttP as being #1.
2) Twilight Princess - It's very dynamic, and wonderful at how it works with what's going on. Nice transitions to trouble / fighting themes, and excellent 'downtime' ambient music awaiting your return to action. The more triumphant Epona theme is a wonderful addition as well.
3) The Wind Waker - Great seafaring music that really gives a sense of wonderment to exploration. It really does feel like a journey on the high seas. This is something I don't think Phantom Hourglass' theme really got as much. It was a secondary theme to this one, but just not as 'right'.
4) Majora's Mask - I love the somewhat sinister opening to the theme, and the sense of urgency behind it. Plus it's a great classic rendition!
5) Link's Awakening - I love the opening addition to the main theme and also the follow up piece that was added before it transitions back to the beginning of the song again. It's really too bad those additions didn't make it further into the series, but then the main theme has pretty much been dropped as an overworld theme.