I got a 6800 GT DDL card directly from Apple and returned it a few days later - it was insanely noisy, which was surprising given the size of the cooling solution. I swapped it for the ATI X800XT and its MUCH MUCH quieter, close to silent.
Basically the ATI adds a very very slight increase in noise of the G5, and the system+graphics fans spin up as necessary under load (not by a huge amount thankfully). The NVidia card on the other hand doesn't seem to affect the system fans, but its own on-board fan is spinning very fast ALL the time.
Another plus for the X800XT is that there is a freely available overclocking utility ATIccelerator which allows you to get a bit more performance out of the card. Add to that the control panel which allows you to modify the performance/visual quality settings (something the NVidia card sadly lacks) means that although I prefer NVidia cards on the PC Platform, the ATI card seems to be the better engineered, better thought out card than the NVidia on Mac OS X.
Personally, I'd go for the ATI. You'll save a lot of time returning cards the way I had to. Performance seems to be equal, if not better than the 6800GT