you have to excuse me. English is my third language. I'm not sure entirely what you wish to know.
In terms of computing power, the GPU is always ahead of a CPU. So naturally the GPU is better. However, GPUs are not as stable as the CPU and can have problems with errors in the calculations. So the bigger the project is, the better the CPU could compete with it. Especially if stability is the main concern. ECC memory can boost stability quite a bit on server platforms. A CPU is build to run 24/7 under full load; the GPU can have problems with that after a few months...
Therefore the initial idea by Stanford was to give small WUs to CPU and GPU, mid-sized WUs to GPU and big-WUs to multi-socket CPU systems. At least that was the idea one or two years ago when the new "big-WUs" exclusively for 16+ core system for F@H were released. Since the CPU (even a multi-socket system) is much slower than the GPU, CPU WU were given bonus points. The quicker you finish a SMP WU the more bonus points you'd get. The idea was to make SMP-folding interesting. Otherwise the GPU would just dominate, and some of the WUs wouldn't be folded regularly.
Now fast forward to today. SMP-WUs still get bonus points and hence score phenomenally in terms of PPD although the computing performance is not there. The really major thing in the last few months was Stanford's attempt to really get OpenGL properly supported for folding. AMD/ATI cards now
FINALLY got the proper support and finally can fold with proper results. Just a few months ago a 7970 which in terms of computing performance beats pretty much any nVidia card, was getting only a few thousand PPD (which is like a GTX 285 or something nVidia had a hand full of generations ago).
Due to the proper OpenGL support, nVidia is no longer the major favorite for F@H. A 7970 will now get up to 100k PPD while a GTX 690 will get "only" 40k PPD; The Titan is @ 50k PPD;
Just due to the OpenGL support things have changed on a major scale over the last few weeks. Will those PPD maintain? I don't know. AMD WUs are still in the test-phase so there might be some adjustments in terms of PPD;
The CPU PPD and WUs won't change much I hear. So I should be able to give you pretty precise numbers for pretty much any 2P or 4P system you're thinking of getting. I'm pretty confident that I won't miss by much.
AMD-GPU PPD in 2 months could be different. I really don't know if or when they will change anything there. nVidia GPUs are just not worth investing in anymore. At least from todays standpoint. Whether they will do some adjustments in terms of nVidia WU PPD, I don't know... They did release some beta-WUs for nVidia which had bonus points too. Either way it doesn't look that good for multi-socket folding@home systems. They now still have the best PPD/Wattage consumtion ratio. How long this will stay like that nobody really knows...
A multi GPU based system is a decent alternative. There is not much use outside of F@H you can find for a 4P system. (if you can think of something, do tell me. I'd be happy to give it a try)
If you get the GPU-based folding farm the PPD/wattage consumption will be worse (that's for sure) but you can easily find another occupation for a multi-GPU system compared to a multi-CPU system if you wish to change things up. And keep in mind that updating GPUs is much easier than updating CPUs...
I'm not sure if that answered your question. I hope it did.
