We've covered this issue on MacFixIt a few times before - an annoying clicking noise on some PowerBook G4 and iBook models that seems to occur in most cases when the system is muted and an application attempts to generate sound. Sometimes, when the volume is up, the clicking noise is followed by the normal, delayed sound.
Some users have found that the application KeepSoundAwake, which sits in the background and plays a "silent sound" every 20 seconds, thereby preventing the audio hardware from sleeping, resolves the issue.
In-house, however, we found KeepSoundAwake simply generating the clicking noise every 20 seconds when it attempted to create the "silent sound" while volume was already muted.
A much easier solution, we have found, is to simply attach a pair of headphones or a dead-end line-out jack to the clicking PowerBook. Doing so keeps the machine quiet when it is muted, absorbing the clicking noise so the speakers are never activated.