All flutes can be used to play tunes like normal instruments. Then they have additional effects if used properly.
http://pokemonuranium.co/forum/showthread.php?tid=816&pid=11537#pid11537
Creshire's flutes are a little different from canon thanks to the rules of the game. The first two are best used when I list the Encounter slots.
The White Flute, which the Survivalist called the Clear Flute, calms wild Pokemon. In game terms, this mostly means they are more easily defeated in combat - they'll use less strong moves and have effectively lower stats. At GM discretion, they may also become easier to catch.
This flute requires a little potash to craft, freely available wherever ash can be found.
The Black Flute is more like obsidian or slag. It makes wild Pokemon temporarily stronger and give more XP. Many will be harder to catch and might end up with stat Surprises or stronger moves.
The Green Flute can remove Sleep and Infatuation and Confusion instantly, but not in battle. It requires only ash.
Any other color Flute can be a low-tier valuable item, in which case you do need a roll to see the value.