I believe this is the infamous chirping power supply issue. Please read the following KB article in its entirety and see if it describes what you're hearing.
http://docs.info.apple.com/article.html?artnum=86523
My parents have a dual 1.8 GHz G5, and it will emit these noises when using the mouse wheel to scroll in Safari and if I recall correctly, it's done the same the few times I've used After Effects on it. However, it's not related to AE specifically; it's just that certain tasks in AE (such as scrubbing the timeline) make it noticeable.
If your machine doesn't fall within the serial number range that's eligible for power supply replacement, you can download Apple's CHUD tools, which will install a Processor preference pane in System Preferences. That preference pane has a checkbox to disable nap, which should alleviate the problem somewhat. You have to redo this checkbox every time the computer is restarted, though.
I believe the current version of the CHUD tools requires OS X 10.4, but there should be older versions that will support OS X 10.3. You'll just have to dig around in
ftp://ftp.apple.com/developer/ToolChest/Testing_-_Debugging/Performancetools/ to find a version that works.