If you're going to use ZFS, you'll need at least 4GB of RAM, if not more, and you won't have to mess with onboard RAID, which is a bad idea to use anyway. 8GB of RAM seems to be the recommendation for a low end NAS using ZFS.
Of course, if you're not planning on using ZFS an Atom or E450 with 2-4GB of RAM will work fine.
I'm not sure if you've read it, but the FreeNAS Hardware Recommendations
would be a good section to peruse. They have an interesting tidbit about Samba being single threaded, so if you're going to need smb/cifs shares, you're better off getting a CPU with better single thread performance.
Looking at CPUs the Intel Pentium G640T and Intel i3-2120T look interesting as they are 35W parts.
Your requirement for 6 SATA ports narrows down the motherboards choices, and it ends up putting you in the $200+ range of desktop motherboards. At this point, I would step up to a server board, and looking at them, they are a little cheaper with Intel NICs. Asus has a nice board that might work with either of the processors listed. (Link
) I'm not 100% sure they will work, as it's a little confusing how they listed the supported procs, but they might.
Something else to think about is the NIC. Intel NICs work great, and I highly recommend them, especially the server stuff. It's an extra expense, but they are well worth it. You don't need to think about this if your buy a board with them built in.
As for cases, get whatever has hot swap drives or will accommodate a couple of hot-swap cages, like this one
. I'm not sure if that one actually works, but it's the first one I found.