Official Nintendo Magazine has confirmed that Spirit Tracks will contain an instrument for Link, and you will be able to learn different songs for it that will unlock different things, in the style of the main console games.
On the downside, it appears you’ll have to use the DS microphone to play the songs, meaning that attempts to play the instrument in public may result in everybody nearby thinking that you have lost your mind.
“You’ll be able to use your DS microphone and stylus to help Link to play the Spirit Pipes in his new adventure.
They’re basically like a set of pan pipes which you can play to summon special powers. To play them you blow into the DS microphone while cycling through different coloured pipes with the stylus.
Before you’re able to visit a temple, you have to search for one of the land’s guardians, called the Lokomos, who will teach you a song which restores the tracks to the temple. You’ll then be required to listen to the metronome to keep to the rhythm.”