I've got a G4 with two hard drives, one running OX the other O9. I've got DP 3 on the O9 with 512 or ram. (I think I have twice that ram on OX). I'm also using Waves Gold plugins, and they eat up a ton of memory. On a couple of tunes I keep getting the message to raise the buffer. The DP3 default is 1024 (or something close to that). I had to raise it to 4000ish to play the song without crackles.

My questions: What are the issues of changing the buffer settings up and down for various songs? Is this hard on the drives? Should I be defraging the disk after changing settings? If I increase the ram on O9 will it solve the problem of having to adjust buffer settings? Is there any way to utilize the ram on the OX disk?

It sounds like you are using virtual memory or a RAM disk in OS9. DON"T!

Using disk-based RAM will result in much slower performance. Turn off virtual memory and your RAM disk in the memory control panel.

Unlike OS9, OSX dynamically allocates memory, meaning that all of your physical RAM is available to whatever application may need it at any given time..

To allocate more RAM to an application in OS9, highlight the application in the Finder and hit Command-I (get info), selecting the 'memory' tab in the resulting window will show the minimum and preferred memory allocations for that application. Cranking up the preferred number will allocate more RAM to the application, but only if it has not already been reserved for use by another running application.

Virtual memory is turned OFF. And I have played around with the Ram allocation, but haven't seen a significant improvement. Digital Performer runs with MAS and so they suggest allocating smaller amounts of Ram to DP to allow MAS to use more ram in the background. I'm at a loss as to what to do to improve the situation.

Then it sounds like you should allocate more memory to MAS.

No, don't give DP3 more memory.
I don't know how big your project is.
But not more than 200 MB for DP should be plenty.
In fact the setting can be less than that, if the size of that project isn't big.

DP's memory and MAS are different.
You set the memory for DP just enough for open the project and do the MIDI.
Once you start using audio plug ins, what is left in your computer (DP & OS 9) will be used for that.