It should be used as a weapon. Not like hit enemies over the head, with it

but use the songs as weapon spells. It seems like all the instruments are for are just warping around, with the occasional awesome use ( WW's controlling of the statues, medli, and makar to beat the temple). An example could be like as song like "Ballad of the Barrage" If you played it, a barrage of notes/music would hit the enemy. These could even be used as an alternative to items in dungeons. Not all the items of dungeons, but maybe a couple of em. They also wouldn't be too overpowered. They could just have the power of an item.
For this to work, it would be kind of a hassle to play a song, wait 10 seconds for the "song played" animation, then the spell. They could make it like a quick selection. It could be placed where you would put your normal items (bow, boomerang, etc.), and you could just press that button, and it would play the song, without all the extra animations. or if this is for wii, and if they used a wind-waker esque baton, you could run around the enemy/ boss, while quickly conducting the melody. This would also add some difficulty to the games as well.
The main reason why I brought this up is because it seems like even though the game is named after an item, it really shouldn't be. Even though the windwaker was used throughout the entire game, it wasn't like the master sword in power. They might as well name both
OOT and WW "The Legend of Zelda: The Master Sword" I think that the windwaker/ ocarina/ other instruments should hold the same power as your arsenal of weapons.