Most of this is similar to the Backblaze Storage Pod, except that I don't need that much space (yet), I need a free standing server, and they don't sell the case they made. I also only have about half of the drives, but I'm getting more as needed. This first bit is like the starter kit. Most people building something like this can get an old case and some drives they can use at first before they expand out of it with more drives. These parts should cost <$250 shipped. Motherboard - six SATA ports and three PCIe 1x or greater slots. Onboard video is a plus. Lots of options for <$100.
CPU - I like the Intel E3300, which is a Core2Duo Wolfdale core for only $50. It's cheap, fast, and low power. Socket LGA 775
RAM - I find 2GB is more than I need. <$50.
Power Supply - 300W of an 80 PLUS BRONZE will get you there. The recent high capacity/lower power drive review showed peak consumption was at spinup, and varied from 14-19 Watts. 12x19W=228W, which should be below the threshold for a decent 300W with the rest of the system being powered too. If you're worried, 350W has plenty of headroom. I got a SeaSonic SS-300ET for $40. EDIT: One of my drives got a bit flaky, and checking the model number on the internet showed it was very sensitive to voltage. I replace the power supply with a SeaSonic S12II 520W for $73 and the problem went away.
This bit is everything else, minus the drives themselves. You wouldn't actually need to buy it all at the same time, but you do run the small risk of buying one drive cage, and then have them stop manufacturing them. You should be able to get all of these parts in the necessary quantities for <$200 shipped. Case - Cooler Master Centurion 590. It comes with slots for four harddrives, and combined with the cages below can fit 12 harddrives. The cooling is also pretty awesome/simple for the drives. Both side panels come off, so you can route the cables behind the motherboard tray to keep them out of the way. $60
Drive Expansion Cages - Cooler Master STB-3T4-E3-GP 4-in-3 Device Module Hardisk Cage. You'll want two of them. They aren't exactly the same as the one included with the case, but they're close enough. $23 each.
SATA power connectors - 4pin MOLEX Male to (4) 15pin SATA II Female Power Cable. This will take a single molex power connector, and give you a string of four SATA power connectors in a row, which is really convenient for cable management purposes. Monoprice has one for ~$3.50 each, but they're 24" in length, which is annoying. The NZXT CB-44SATA is 8", which is the perfect size, but costs $12 each, which is ridiculous.
SATA controller - Syba SY-PEX40015 two port PCIe 1x controller. You'll need three of them. Sure you could get single 6 port card, but you'd also spend a lot more. These get the job done, and with only two SATA ports per card the PCIe 1x is fast enough. The Syba SY-PEX40032 supports SATA 6Gbps if you want it. I might get a 4 port card (such as the Syba SY-PEX40013) so that I could also drop a small SSD in just for the OS. I got these from Monoprice for $14 each.
Misc - Fans, SATA cables, etc. I don't think the case needs any extra fans, although I dropped a few in that I had around. Non-OEM drives come with cables, but I like to pick up cheap SATA cables in different colors so they're easy to track.
The harddrives are the most expensive piece. According to the recent 2TB low power review, the WD Caviar Gree 2TB and the Seagate Barracuda LP 2TB both appear to be decent options. The Seagate uses 4.5W more power on spinup, but 2W less on idle). I regularly see deals with 2TB low power drives going for $95-99 shipped. $100x12 = $1200. Altogether: $200 + $250 + $1200 = $1650 And that's a highball. Shopping around should pull things as low as $1550. For the OS, I like Windows Home Server. Fully duplicated storage provides 12TB of space, and the new version due out soon will offer higher performance. The cost of WHS is $100. The open source version of the WHS Drive Extender is Greyhole, which has been integrated into the Linux based all-in-one box Amahi, which is free. There are other software RAID1 solutions out there, but I like these because the drives don't have to be the same size. In the future I can replace my 2TB drives with 3TB drives, one drive at a time. Also, don't forget to use a UPS. The power usage of this thing is probably <100W idle, so a <$50 UPS would be fine for most people. There's a lot of peace of mind in that. And cheap 5 port gigabit switch that will push $900Mbps of real data can be had for <$30, which is a worthy upgrade for any cabled computers. Thanks to all those that helped me find the right pieces for my server.