Here are my two cents, as I recently went through a similar process. For what it's worth, it took me over a year of occasional research before deciding on what I wanted out of a NAS system, and then a good hard 40 hours or so of detailed reading and research to settle on the build. The physical build itself probably took another 40 hours (modding and routing cables, swapping fans, figuring out how to best build in a mini-ITX case etc). Configuration of the NAS (from the bios to the software) is another ~50 so far, and likely another 20 from full deployment, but I am pretty new (well, new again) to Unix type systems of any flavor, so there is some learning curve here involved with writing the first shell scripts I've touched in over a decade (not strictly required, but useful to get to know how to use things from the command line in case you need to use it someday). Any fooling with plugins is additional time and effort.
For me, the priorities were as follows:
1) Data security
2) System stability
3) System longevity
4) Speed
5) Plugin features (DNLA, etc)
6) Ease of use/configurability
7) Everything else (noise, form factor, etc)
Items 1 and 2 on the above list led me to ZFS (RaidZ2 or better) and a stable distro with good docs and a large user community. They also required the use of a server class motherboard, and a large amount of ECC RAM (also helping goal 3). Goals 1, 2, and 3 additionally create the requirement for well supported (by FreeBSD in the case of FreeNAS), quality parts, which leads me to Intel server class parts, NICs, etc, and a solid HBA, controller, or JBOD card.
Item 3 addresses quality fans, good cooling, and scalability of the system (adding or swapping drives in the future).
Items 5 and 6 led me to FreeNAS.
Item 4 was less of a direct driving concern, but more of a secondary consideration when picking parts. Item 7 led me to a nice Lian Li case and good quality fans with long warranties.
All of that resulted in the following:
Code:
Case: Lian Li PC-Q25B
PSU: SeaSonic SS-300ET (OEM)
MB: Intel DBS1200KPR
RAM: 16GB Kingston ECC ValueRAM (KVR13E9K2/16I - 2x8GB kit)
CPU: Intel Celeron G555
Flash: Mushkin Mullholland 8GB (USB FreeNAS boot)
HDDs: 6x Western Digital 2TB Red (WD20EFRX)
HBA: Highpoint Rocket 620 (2 ports)
HSF: Noctua NH-L9i
Fan #1: Noctua NF-P14 FLX (Intake 140mm)
Fan #2: Noctua NF-S12B FLX (Outflow 120mm)
Some explanations:
The Lian Li case is a high quality, tool less, mini-ITX design with great cooling and 5 hot swap bays with room for at least 8 total drives (I've seen configurations with up to 10 drives).
SeaSonic power supplies are rock solid, high quality units. 300W is more than enough, and I modified and sleeved the cables for best fit in the small case.
Motherboard is an Intel server unit with dual Gb network ports, support for 16GB of ECC RAM, a single PCI express slot. The CPU itself is the highest clocked (important for CIFS speed and future proofing) Sandybridge-based Celeron, supports ECC RAM, and was less then $75. Quad cores and Xeons are overkill for NAS use, but this motherboard supports both if I ever feel the need for more power.
The HBA is on the recommended list for supported controllers for ZFS under FreeNAS, and was all of $15. If I wish to grow beyond 6 drives, I can always pick up a M1015 and support up to 12 drives total (more than I could indeed fit in the case).
The WD Red drives (providing a bit over 7TB in a RaidZ2) were a good match for my current and future data sets, without breaking the bank. Nearline or true server class drives are recommended, but I cannot justify the cost. I should acceptable MTTDL and failure tolerance with this system, and I spread out my drive purchases between three different vendors and over about 3 weeks to reduce risk of getting a set of drives from a bad manufacturing run or a dropped pallet. My current data set that will be hosted here is less than 2TB, so I have plenty of space to spare at the moment, and multiple upgrade paths if I need more in a few years. All data is backed up elsewhere as well (via cloud for offsite) and will continue to be backed up to on site disks and the cloud going forward.
Noctua fans are high quality, very quiet, and have long warranties. While I've not really loaded the system up yet, the drives sleep (spun down) at less than 5C over ambient (lowest I've seen is 22C). Running I've not seen them go above 35C. CPU hasn't hit more than 42C or so, and idles around 32C. I actually will be turning down the fans a bit to reduce noise and total temperature swing on the drives before I finalize the build.
Performance in testing under CIFS is >75MBps read and write sustained on large (2-5GB) files. iSCSI is better; write I've seen stay over 100MB/s. These are not controlled benchmarks, but were good enough for me to call the build working. I likely won't really bother tuning the system that much given the performance I was seeing, but we'll see how things go as I start to load up the system.
The use of this system is for a home NAS storing media of all sorts, backups of local PCs, drive images, and maybe an iSCSI share to screw around with. It will also serve media via DLNA to multiple devices, and eventually will be the backend storage for a XMBC system.
The only issue I've experienced so far is interrupt storms when I have a wireless USB keyboard plugged in, but as it will be running headless and without input devices in deployment, I've not worried about it.
Hope this helps. My suggestion is to really read read read read, think about your real needs and priorities (come up with a list), and then spend the cash for quality parts if you can.
Good luck!