WCG (World Community Grid) is basically a catch all, and does other things as well protein folding. From what I recall it can do traffic planning for certain cities, or long term estimates of various things. There are studies to help formulate more productive foods or discover new medications and cures for various things, not just cures for protein misfolding. You can crunch on both a CPU and GPU, though the CPU client is far better utilized than the GPU one and can do more in the same time, which is a better use of your power bill and time.
As for Folding @ Home, it is specifically looking at misfolded proteins and why they occur. There are many genetic diseases this can hope to cure, though not directly. Once a cause is found, they still have to look at ways to reverse it. However things like many types of cancer, Ehlers Danlose Syndrome, Alzheimer's and Parkinson's are targeted among many others. If this project proves successful, then these diseases could be eradicated. Aside from finding cures, this program also helps us formulate new theories on the designs and makeup of these proteins. It can help point to new realizations and it already has. I believe there is a page showing the papers (research) they've completed on Folding @ Home. Again, this program can be done on both CPU and GPU however in this case, Folding @ Home makes a better use of GPUs, specifically nVidia. There is an ATI client being made that is supposed to greatly improve how well it already works, but currently the ATI architecture isn't utilized to its full potential. That said, ATI cards it still do an arguably better job than CPUs at folding.
This opens up a true match for the two, as it would help both teams and maximize the time and money you'd put into this. Crunching on the CPU and folding on the GPU is how many members here have gone. However you choose to help, if you choose to help, is up to you though. Any donation you provide would be greatly appreciated.