An atom based system would be a good direction to head in, and without going in a very specialised / very expensive direction that's probably the best you'll do. VIA have some similar chips out that I think use slightly less power, but they're older and far less powerful than the atom equivalents.
I'd personally look at an atom board, solid state drive, high efficiency, small power supply (there are some DC ones around that fall into this category) and turn off everything in the BIOS that you're not using (sound, any onboard controllers and suchlike) to keep the power level down.
Never actually done a lower power build for myself but was thinking about it at one point - it's an interesting one and does shift the focus a lot from conventional building. Good luck with it