I've heard so many people mention this exact situation, that I thought I'd post the answer I found at : http://www.mini-itx.com/faq.asp#Linux0
here, as I haven't seen it mentioned elsewhere, and so I can find and reference it easier.
3.2. What should I do if I have poor quality sound (pops, clicks and squeaks) - particularly when dragging or scrolling windows?
This is caused by X writing blindly to the video card's instruction queue without checking to see if the queue is full. This will lock the PCI bus for about 40 - 50 audio cycles, causing pops, clicks and squeaks. The via82cxxx_audio driver is still somewhat fragile, so it is possible that some applications will fault ungracefully if the bus is disrupted badly enough (e.g. with SDL applications).
You can make X play nicely with the PCI bus by adding
Option "PciRetry" "true"
to the "Device" stanza. Nasty pops and glitches will go away, and system stability will be much improved.