Just an interesting piece of info for anyone who may have experienced similar problems...
I ordered the Dr.Bott ADC to VGA adapter from Apple so that I could also use the DVI to Video adapter on the Radeon 9800 256MB BTO.
In the same day, I replaced a NEC3500A with my Pioneer 107 because I was sick and tired of the NEC's "disappearing disc" problem. I also left my new Shuffle charging while the G5 went to sleep. Subsequently...G5 would wake from sleep with the dreaded grey multi-lingual "you need to restart your computer" message. Every time if put to sleep!
After much permissions repair, disk utility and hardware diagnostic CD shenanigans, I finally remember the Dr. Bott and switched back to the normal DVI to VGA adapter. Problem solved! Something doesn't like the Dr. Bott when it comes to waking the machine. I've read elsewhere that ATI cards can cause problems in this regard if they don't like the physical connection to a display (A Formac 22.880, in case you're wondering).
"Bott"om line, not everyone may experience this problem, maybe this one is a dud for some reason but if you are pulling you hair out and can't find the solution...this may be it!