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It will turn in WU faster but the PPD from a Q6700 will FAR and away more. The PS3 gets about 900PPD and a Q6700 should net you 3-4K PPD without trying real hard. The biggest issue I have with the PS3 as a folder only is the cost and the power usage. For $400 you can buy a better folding only box. If you plan on buying a PS3 anyway (I own one) then the 900PPD isn't to be sneezed at.
The PS3 will turn in a WU (work unit) faster than a C2Q (the usual turnaround is about 8 hours if I recall correctly) however these WU do not have the same point value as the SMP WU that are assigned to the C2Q (if you use the SMP client). The PS3 points end up being about 300 each (@ 3 per day = 900 PPD (points per day) while the C2Q may only turn in 1 WU a day the points on them are ~1200 or so (or more) and most folks can run two instances of the SMP client on a C2Q (using VMware) giving them between 3K and 4K PPD although they are only turning in 2 WU vs the 3 that the PS3 is turning in. It is some weird point scheme that Stanford uses that nobody really understands (I think they have a dart board with point values on it and they throw a dart every time they have a new run of WU)
So you're saying the PS3 actually performs the same amount of work *faster* than the C2Q but gets fewer points for it?

I think I get it now.It's not that simple. The machines don't work on the same work units. The PS3 can only process certain types of work units while the Q6600 is a lot more flexible. The point values reflect this. I think the PS3 is getting shafted with 900 PPD, but even if it was boosted, it will never give you the same amount of points as a quad.
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I think I get it now.
Is it safe to say that the Core 2 will perform more actual work in a day than a PS3, and that's why they get more PPD?
The PS3 right now runs what are called implicit solvation calculations, including some simple ones (sigmodal dependent dielectric) and some more sophisticated ones (AGBNP, a type of Generalized Born method from Prof. Ron Levy's group at Rutgers). In this respect, the PS3 client is much like our GPU client. However, the PS3 client is more flexible, in that it can also run explicit solvent calculations as well, although not at the same speed increase relative to PC's. We are working to increase the speed of explicit solvent on the PS3 and would then run these calculations on the PS3 as well. In a nutshell, the PS3 takes the middle ground between GPU's (extreme speed, but at limited types of WU's) and CPU's (less speed, but more flexibility in types of WU's).