a low power folder/htpc is entirely possible on a shuttle
I have similar plans to yourself and am looking at the SN78SH7
getting a barebone is cheaper. Add your own GPU, HD, RAM and CPU...
The only problem with this setup is if you have a dual slot card, you are limited to using a usb tuner for htpc functionality. If youre not planning on using this with a dual slot card, you could go for a cheaper variant. Of course, you could ditch the card altogether and use the onboard nv8200 for htpc purposes. You could likely use it for folding as well as integrated 8200 is cuda enabled
There are many linux htpc variants. These sre chiefly used by 3 types:
*advanced setups, arch linux severs etc
*people who like the advanced tinkering
*people who hate MS
Feel free to have a squiz around the Linux area at the htpc site
I contribute at. I have a cataclysmic personality clash with the guy who presides over this area, so you wont see much of me in there
Lots of great info though...
Alternately, you could get a ps3..games, folds, bluray and pvr functionality with playtv addon.