My main folding rig is a slightly OC'd Q9300 running Debian Squeeze. It is also used as my file server, but it spends pretty much 100% of its cycles folding. I recently upgraded the video card on it to a GTX560 Ti and use it under Wine.
From a tip point of view, I have spent quite a bit of time tweaking the gpu setup. Unlike the comments on the main forum, I actually went the other way and give it as much CPU as it wants. The main forum leads you to believe it consumes too much CPU and you should either use an environment variable or a script that does that to "tune" your CPU usage. My experience using that envar or script kept my cpu utilization down to about 20% (of one core) but only gave me about 8k ppd. I went the other way (didn't set the envar and actually upped the priority above the normal apps - I run it 'nice -n -1 wine Folding@Home0Win32-GPU.exe
-forcegpu nvidia_fermi'. It uses 27% of one core and produces 12720 ppd - nice tradeoff.
Now I don't use this system as a desktop system so I don't know what it would do as far as introducing lag, etc.
I also found the GPU folding more sensitive to the CPU clock than I expected. From what I understand the only way the GPU can perform at maximum is to keep it fed with data and it needs the CPU to do that. The faster the CPU the better (even tho we are not using 100% of it).