A couple of other points to consider that are on my mind (and I have not run FAH for a long time) are:
Don't GPUs (the graphics cards) play a far more important role in processing protein folding software tasks as above?
And, have you considered the
Playstation 3?
I really don't know anything about all this as it currently stands but I can see there are whole sections of FAQs devoted to the subjects at FAH:
http://folding.stanford.edu/English/FAQ
Also, there are a great many Folding Forums and these have a lot of dedicated people who can give some expert up to date advice. I think it should be okay to give a link here to Bit Tech:
http://forums.bit-tech.net/forumdisplay.php?f=111, they have one such forum and the advantage is their site is totally geared up to computing, including 'folding' and building custom specs, choosing and sourcing components. I think you should not overlook the role of the graphics card but maybe things have moved on with the latest crop of multi-core central processors?
Lastly, you can get SSDs relatively cheaply these days as prices have fallen considerably in the past month. A Crucial M4 128GB SSD is not a bad choice for price/performance:
£87 example at Amazon (be sure to update firmware first though). Oh, and my hunch is that you should be able to buy a relatively small case and modest system spec and still have very good Folding performance without needing to worry too much about super efficient cooling requirements above and beyond a few fans. It just depends on the hardware and how hard you intend to run it and this is why you need to read up on other people's experience in building this niche quiet and high performance design really - fans and heatsinks can be replaced but that's a hassle you can avoid if reading about other people's experience beforehand.