I would avoid the atom. It is quite enough for file-server only duties... but let's say you wanted to run some "services" like PDF, OCR, http-server (even if just for LAN and not open to internet), then you will find the Atom a little disappointing. I run 2x D2700 supermicro 1UE racks, one as a RAID1 fileserver, the other as a web-server exposed to the internet. They both manage fine... but the webserver doesnt do video and has MAX only 20 users (it's a private website). I wanted to run a watchfolder with PDF-shrink-and-OCR service, and also HP Digital Sender Service (pretty similar function... scan, OCR, PDF) but it was so too slow on the Atom, I had to run it on a desktop.
I remember seeing recently on the supermicro website, they have a MOBILE CHIPSET ITX board. It runs idle near-nothing power, but when demand hits, it will significantly outperform the Atom.
Let's see if I can find it...