I haven't encountered the sound problems yet. The early SB61G2's had a motherboard flaw (capacitors as I recall) that caused the on-board sound to break up, drop out etc. There was a Shuttle RMA set up to fix the problem for anyone willing to ship their box back. The problem was corrected for later (starting in Aug.2003??) SB61G2's and is apparently fixed on those currently shipped. I guess it is possible to end up with one of the early releases if you buy it at a small shop where the inventory just sits around. Those from volume sellers, Newegg, ExcaliberPC, etc should be the corrected model by now.
The other problem that Psycho mentioned has to do with a grounding issue for the front outputs (I'm not using them either), and there is an inexpensive do-it-yourself permanent fix posted on the SFFTech XPC Forum.
For general use, the on-board sound (Realtek) is basic and probably sufficient. If the focus of your system is music, especially through headphones and/or you are an audiophile, you would do well to pop a sound card into the PCI slot.
All in all, I have been pleased with my 20th Anniversary Edition for the month that it has been running (crosses fingers here).