As a Shuttle devotee for many years - don't do it. It's not worth the loss of expansion, the loss of capability, the loss of choice in motherboard, and the extra cost.
More importantly, you won't meet you goal of quieter because if you put performance components into a Shuttle, you are going to be starved for ventilation and cool air. The videocard fan will run noisy, the powersupply fan will run noisy (and efficiency will go down so you'll get even less wattage).
A performance Shuttle system can be built if done right but it takes a lot of effort and creative modding to do so. I wouldn't suggest it for anybody but a devout enthusiast.
If SFF (small form factor) really is your goal with a combination of HTPC and performance, I would recommend going up a bit larger to make things easier for you and go with MicroATX. Check this forum for ideas:
http://hardforum.com/showthread.php?t=759688&page=31