capcave. If you are stuck with Windows then, yes you have to use x86.
I'd be happy to advise what the linux equivalents are to do the same things you are doing with your windows software, but there is no denying that changing to unfamiliar software is more work. It depends how serious you want to get into 2W territory :-) I assure you it will be satisfying in the long term, as you get infinite flexibility.
Re the PSUs for ITX boxes:
IT is difficult to find out what the low-load characteristics of switch-mode PSUs are. A page like this is fairly helpful:
http://www.mini-box.com/s.nl/sc.8/category.13/.f or (with UK plugs:
http://www.mini-itx.com/store/?c=10 )
I really like the pico-PSUs that fit in the top of the ATX connector:
http://www.mini-box.com/s.nl;jsessionid=ac112b6b1f43000fed76414a4b63a2679f6e38d7d958.e3eTa3aSaxmTe34Pa38Ta38Pbhz0?it=A&id=417&sc=8&category=13which claims 96% efficiency. I don't know if that is still true at 5W