One of my first thoughts with this prompt has been linking the sound gameplay with a "vibration" system. Nothing naughty, just like the player must use appropriate sounds to cause liquid ripples of the right size. This video http://www.youtube.com/watch?v=EZT4F3J4LxA
kind of shows what I'm thinking of.
It could be like a GarageBand type setup where the player can use any notes and composition they wish, but the music has to have certain frequencies at certain moments to solve puzzles.