I am having the same fan problem. I thought it was the disk drive. I have tried running no software other than Garageband but that doesn't help. So I don't think it has anything to do with the number of programs or does it? Does Garageband use a lot of resources on its own that causes the fan to spin? Perhaps. I'd love to get Audacity working but I can't get it to work (need more sleep and I need to try it again!).
From Berlind’s PodTop.:
The iMic is cool, but I have a serious EFI problem when the Powerbook's fan comes (to cool off the processor) that results in a noticeable high pitched whine in the background of my recordings (and unfortunately the fan cranks up ALL the time with all the stuff I'm running on this baby).