I've a few comments on your plan, based on my own experience of building a similar system (low power, file server, mp3 server (slimserver), ubuntu). You can see we're on the same wavelength. In my case, I wanted to reuse as much of what I had lying around as possible (processor, motherboard, 60GB HDD, PSU). The resulting system is:
AMD Duron 700MHz processor, on the cheapest board I could find to house it, a PCChips M811 Skt A.
Maxtor 60GB ATA (system disk)
2 x Samsung 320GB SATA, housed in an IcyDock MB235SPF RAID enclosure, connected via an unbranded PCI SATA card.
Nexus "Real Silent" 350W PSU
I give you this is so you can put my comments into perspective:
Low power?
Your 500W PSU doesn't suggest a low power solution - I suggest you do some calculations to estimate the running costs. My system draws a steady 160W, which I'm not happy with. For me the cost of electricty makes this unacceptable - around 100 UK pounds, 200 USD per year to run, and it's only going to get more expensive. So I'm having a rethink. The desire to save money by reusing stuff I already had may not in the long run be the best idea. I would like to cut the power used by 1/2 or even more. I've seen claims of systems that use just 10W (check out the NSLU2 for interest).
Use power management to the full
The vast majority of the time the data HDDs will be idle, so ACPI should be allowed to power them down or you're wasting energy and money. My choice of SATA drives was a deliberate future-proofing decision even though the motherboard does not support them. It meant that I had to buy a PCI SATA card (the data transfer rate is limited by PCI, but good enough for this application). The problem is that it doesn't seem to be any power management for the HDDs, so the they are always on. Again, what seemed a saving with the old motherboard now doesn't seem such a good idea. But a new motherboard also means a new processor, memory...
RAID - do you need it?
I originally thought that RAID was what I wanted, hence the RAID enclosure (although you don't have to use it in a RAID configuration, it's just a convenient way to house multiple HDDs that you want easy access to). When I thought about it some more, I realized that RAID really wasn't necessary. RAID simply guards against HDD failure, which in reality is rare. I've worked in the computer industry for decades - I had my first IBM PC in 1981 and have countless computers since then - and have never suffered an HDD failure. RAID is useful if your data is critical and you can't afford to lose anything between backups. And that's the point, RAID is not a backup solution. RAID will faithfully record the mistaken file modification or deletion just as any other disk will. You still need a backup strategy for RAID disks. The good thing is that a backup *does* provide a lot of protection against an HDD failure.
So now I just use one of my SATA HDDs as shared data. The other is just a backup drive. The data drive is replicated to it using RSYNC driven by a cron task. Frequency of backup depends on how static the data is - mine is relatively static, so I have it set to once a week. But this could be changed to daily if needed. Since the backup process is automatic, it's easy.
To complete the backup strategy, I intend to get another backup HDD so I can have an offsite backup (you never know when that 747 will strike..). It's easy to replace the drives in the IcyDock enclosure, so I can alternate the backup HDD. RSYNC will always bring the current backup HDD up-to-date.
Also, don't forget that all the drives in your RAID array will need power when in use - obvious, but it's all cost. My approach only has the one data HDD active, the backup drive is almost never used (assuming power management of course!!).
I hope this is useful.
Chris