Here's a commercial solution based on the Atom:QNAP Announces the World's First 4-Bay Intel Atom-based NAS - TS-439 Pro Turbo NAS
QNAP TS-439 Pro Turbo NAS is the first network-based storage unit using Intel's power efficient budget processor Atom. The processor is clocked at 1.6GHz, paired with 1GB RAM and delivers dual Gigabit LAN ports, five USB2.0 ports, two eSATA slots and a bunch of RAID configuration possibilities. The unit has room for four 3.5" SATA harddrives and QNAP promises up to 6TB of storage, which should go up to 8TB with the new 2TB harddrives that just arrived.
Pentium M boards tend to be more expensive. You could probably buy an Atom board complete with processor
for less than the P-M mobo alone would run you.
A P-M system would have better CPU performance, but If this is just for use as an NAS, CPU performance doesn't really count.
Intel has decided to artificially limit features on the Atom boards so as not to cannibalize their higher-profit lines, so any board you buy check for number of SATA ports and number and speed of network ports.
Is two drives it, or might you consider expanding later on?
The D201GLY2 has only one 10/100 network port. It is not actually an Atom, but a predecessor. If it meets your requirements, and you can find one cheap, why not?
The following prices are from logicsupply.com. Your mileage may vary.
Intel D945GCLF single core ATOM board has one 10/100 network port and two SATA ports, at only $77.
Jetway NC92-230-LF Atom board has gigabit, two SATA, $105.
MSI IM-945GC dual-core Atom board has two gigabit ports and four SATA ports, but costs $167.
An Atom board would use less power and crank out less heat than a P-M board.
mounting the board: I've never had a Shuttle. No comment.
Power supply: I think it should work. Most mini-ITX boards take a 20 pin power connector, except a few with on-board DC-DC that take a single 19V plug.