The thing of interest about folding proteins is what happens when it screws up and misfolds. (If I understand the issue, proteins "fold" as a normal part of forming themselves, but if the protein "mis-folds" nasty things can happen). Misfolded proteins can cause Cancer, Alzheimer's, Mad Cow, and Parkinson's disease to name a few. By downloading and running the Folding @ Home program you (OK.. your computer) become a participant in discovering how these things work and ultimately aiding in the discovery of medications that will eventually cure these diseases.
At this point you're probably wondering why Stanford and Pande Group should pucker up and kiss my tush, because what they're doing is pretty cool and on the surface it makes everyone involved get a warm fuzzy feeling. Here's the thing... discovering a cure or better treatments to these diseases is not only a great humanitarian effort but also an extremely lucrative one. The Pande Group is nonprofit and says that it will give the data freely to whoever asks for it. You KNOW that Pharmaceutical companies are just salivating to get their mits of free research. Heck, why should they spend their precious research money when they can get it funded by government grants (ie. your money), and data that has been funded by your computer processing power, electricity, internet connection and time. I'm sure that they'll recognize your contribution by making the cure affordable for everyone.
One of the first distributed computing public programs that I can recall is SETI @ Home... which enlisted computer enthusiasts to use their computers in the search for extraterrestrial life. The SETI @ Home project was innovative because the project itself was underfunded and losing scientific funding yearly. By thinking out of the box and seeking help from interested volunteers they were able to continue their research. In contrast, the search for a cure for Cancer, Parkinson's and Alzheimer's disease is not a fringe topic. It's big business. It doesn't make sense to me why this kind of research needs your and my help. The whole thing smacks of cost cutting and maximizing profits. Why pay for something when you can take advantage of people who will happily fund your project for you.
Sony's advertising they are taking part in this project seems like opportunistic marketing... "Not only is the Playstation 3 a superior machine but when you get one, you cure cancer." Who (besides me) is going to put a negative spin on that! Eat that XBox 360! All this good PR is certainly worth making a 'screen saver' available for free download.
So, if you're one of the anticipated thousands who are going to install this on your PS3 - please, feel good about your contribution. But if you'd really like to make a difference, why don't you volunteer at a shelter for homeless people or donate blood? Those are truly neglected, underfunded and needed services.