Most important thing is what do you plan to do with the server before chosing hardware, for example you running VM? a pure MediaServer? a Backup Server for clients? will it transcode?
So for a REALLY long time I've wanted to build my own nas to replace my Qnap which is too slow and not enough storage space. I know I wont get the same low power consumption as my qnap, but I still want to go as low as I can without sacrificing speed.
Have you considered the higher end of QNAP? its ok to want to build your own, if its for budget or even for the hobby of doing it, but if you are happy into how QNAP works, then i would suggest to stay with them. I had a very hard choice when i build my server, as i did test Synology (i still own a DS111) and to me it was amazing, easy to setup, did all the things i needed, except transcoding and the space was limited, this two reasons were the main things that made me do my own server, but i still have regrets, so think about this before you commit into a new OS. Test it before, FreeNas is free, so you can even do a new partition on a pc and test it before you buy all the new hardware.
When picking parts how do I calculate or guesstimate what power consumption will be? Approx 5 watts/drive is all I know.
Expect around 10-20W for a efficient motherboard and if the cpu can be downlock by the OS, like windows (not sure FreeNAS), around 10-15W for a HBA/Raid card, around 5W for 5400rpm on idle, USB devices can increase a little depending on what you are connecting, my server usually is headless and nothing aside form the network is connected to it, i usually control it via Remote Desktop, i think freenas manages via a webpage (not sure though).
Vicotnik's build says Idle 24W which I would be really happy with but it uses Intel DH77DF, and thats discontinued
His board doesnt support ECC, is more a consumer level motherboard, so here is up to you. There are some motherboards still in the market in case you want an intel and dont care about ecc (i do recommend it),Intel Boxed Desktop Board DB85FL Micro ATX DDR3 1600 LGA 1150 MotherboardIntel Boxed Desktop Board DH87RL Micro ATX DDR3 1600 LGA 1150 Motherboard
But the important thing you need to decide is weather you need a Server class motherboard, some of them have tons of features that you might or not use like IPMI, some of this features do increase power consumption, so research first what you need for your server.