To send Ghosts through the Scareway
In the episode The Ones Who Saved The Future (Part V), Prime Evil gives a brief description of the Bone Troller's abilities. B Flat takes Hauntquarters into the past, F Sharp into the future and middle C zaps a victim of Prime Evil's choosing with a lightning bolt.
There was also a special little tune that could be performed to activate the Ghosterizer Ray, a beam with which living beings trapped in the Zap Zone could be turned into ghosts. This particular spell could be reversed by playing the Ghosterizer melody backwards.
Apart from sending Prime Evil's ghosts through time and space by way of the Scareway, the Bone Troller could be used to spy on other beings across time and space, as a means of communication.
The Bone Troller could also lift off from it's place in Hauntquarters to become a flying platform which Prime Evil could use to chase his enemies.