http://www.evga.com/forums/tm.asp?m=100498063
That is the best guide I have found for setting up VMWare and notfreds.
Although instead of setting the priority and affinity manually through task manager(meaning you'll have to do it every time you start the clients), I manually set it in the folding.vmx file.
For a quad-core cpu, to run two instances of VM, add the following for the first instance:
priority.ungrabbed = "idle"
processor0.use = "TRUE"
processor1.use = "TRUE"
processor2.use = "FALSE"
processor3.use = "FALSE"
And for the second instance:
priority.ungrabbed = "idle"
processor0.use = "FALSE"
processor1.use = "FALSE"
processor2.use = "TRUE"
processor3.use = "TRUE"
I also am running a program called WinAFC to automatically set the GPU cores to high priority, making sure the CPU cycles get done before anything else on the CPU, especially the CPU clients.
Doing these two things(Using VMWares instead of Windows SMP, and using WinAFC to auto set GPU client to high priority and the affinity to use all 4 cores), I have increased my PPD from ~4500 to ~7750+(the + is dependant on how much I use my computer throughout the day. If I don't touch it, I easily hit 8000 PPD). Those numbers are if I fold 24 hours a day. This is rare, because this is also my gaming rig.
I am running a Q6600 and an 8800GT; no overclock on either component.