You seem to be aiming for the setup I have. I'll describe it. Prices in Canadian dollars.
Intel Atom (don't know exact model) - about $90
Case with integrated PSU - about $50 (switched out the PSU though, with the one in my desktop, when I found it couldn't handle a DVD drive that I put in later)
4x 1.5TB Samsung HDDs 5400rpm - about $600 total at the time, now about $350-400 total
1x 500GB Seagate HDD as boot disk, can't remember speed but it's probably 7200rpm - about $50
Ubuntu 10.04 (started on 9.04 and kept upgrading)
1 PCI SATA RAID card that connects up to 4 SATA devices - about $30?
1GB DDR2 RAM - about $40
IDE DVD writer - I got this free, but they cost about $20
No UPS - actually I had one that blew due to overload when the power died (basically I just plugged everything into it, though "everything" consists of two towers, a monitor, a wireless phone, a printer that wasn't powered on, and speakers that weren't powered on). It cost about $70
The RAID card isn't supported in Linux, but the drives are still readable, so I use mdadm. The system can't boot off of the drives, especially since they are in a RAID 5 array in mdadm, so I have the fifth drive installed, and that's where Linux is installed.
The parts above are a hybrid of things I bought in different places. The 4 Samsung drives came from Newegg, the DVD drive I had lying around, the boot HDD I got from a local supplier, the UPS came from TigerDirect, and everything else came from a second local supplier.
This setup has lasted about a year now (I built it August 2009, but setup of everything took me a few weeks, into September). No problems so far. It was a good way to learn Linux.
Remember you'll have to install lots of stuff, like Samba and Mdadm, to get this functioning properly with Linux. In the end, it's well worth it, especially if you lack Linux experience and want some.
P.S. I've never heard of a PSU integrated onto the mobo. Does that exist? I thought they were usually only included in the case.