Hi kesh,
Ok, first thing, since I gather you are a grad student doing this for a professor and will be handing this off to "the next guy" at some point I would urge you to document, document, document what you are doing. Start with defining the problem you are trying to solve, propose the solution, get the PI to sign off on it and then detail your build...it's good practice for the real world and "the next guy" will thank you for it. After the build is done & in use write up how it worked out and what you would do differently.
Next, read this to get familiar with the RAID types:
http://en.wikipedia.org/wiki/RAID
And read this for more info on ZFS:
http://en.wikipedia.org/wiki/Zfs
Briefly, you have mirrors & nested mirrors, raidz which is like RAID5 and raidz2 which is like RAID6. Raidz can loose 1 disk, raidz2 can loose 2 and still preserve your data.
The on-board SATA controllers are fine and there's not really any reason not to use them or to look at an add-on card till you need more than what's on-board. Both Intel & AMD make fine SATA controllers. People run into trouble with the cheap controllers or when they add a PCI controller that saturates their PCI bus, you should not have that problem with a box the size you are looking at.
Read through this thread:
http://forums.freenas.org/showthread.php?27-AMD-E-350-Thread-(now-in-new-forum-)
For some other FreeNAS users experiences with the E-350 boards. Best I can tell these boards provide enough horsepower to saturate a gig-e interface, but keep in mind I have never actually used one.
Personally I use an AMD 790GX board in my NAS, intially with a 4850e proc and currently with a PhenomII 940 left over from a system update, which is so much more proc than my NAS could ever use. I like the GX boards because they have on-board graphics with dedicated memory so I'm not using system memory to drive the BSD prompt.
As for using the box for other services....you are going to run into a couple of problems. First, FreeNAS8 doesn't really allow you to add software right now. There will be a package manager that does so coming soon but it is not available yet. That's kind of one of the big sticking points between FreeNAS 0.7 and 8...if you have been using 0.7 you have had the ability to do all sorts of additional tasks with your storage box, but 8 is based off a special version of FreeBSD called nanobsd that is geared toward embedded installs that makes supporting additional software more complex.
Personally, to be blunt, this is a storage box...use it for storage and nothing else. You want this thing to hum along serving files. If you want to add services later just get a second box and give it a NFS share from the FreeNAS box
As for case recommendations, I haven't really been keeping up with the market as I have a *ton* of Antec Solo cases left over from lab machine refreshes. I adore these cases:
http://www.newegg.com/Product/Product.aspx?Item=N82E16811129018
Quiet, very well finished, 120mm fan in back & 2 92mm fans in fron.
PSU: I'd shy away from anything with basic in the name, that's just me. For something close to that price (if you can deal with rebates) I'd look at these:
http://www.newegg.com/Product/Product.aspx?Item=N82E16817703026
http://www.newegg.com/Product/Product.aspx?Item=N82E16817139020
http://www.newegg.com/Product/Product.aspx?Item=N82E16817151096
You can probably go with something smaller with the E-350 board & 4 drives, I'm guessing you would do well under 200 watts even running full bore, but I'm a big believer in overbuilding & paying for quality PSU's.
Flash drive:
It's tough to screw up a flash drive these days that should be fine. You only need a 1Gb drive for FreeNAS right now, but this is also the least expensive componet anyway.
Memory:
Gskill is a good manufacturer, I have no problems with them. Personally I would spec some ECC memory if the board you select supports it. Check the compatibility list if there is one. There is no such thing as to much memory, especially in a ZFS box, whatever you select, get 8Gb minimum...memory is so cheap these days there's no reason not to.
NIC:
Nothing wrong with the Intel you have selected. Personally I have a big bias against Realtek, always have so if you plan on doing 2 links you might want to look at one of these:
http://www.newegg.com/Product/Product.aspx?Item=N82E16833106015
Please note, that is my own strong personal bias showing through here, ther's no reason to think the on-board shouldn't be perfectly fine, but you asked!
As for your case concerns, I'm a big fan of paying for a quality case, mostly because they tend to stick around...I've been using my Solo since the AMD 3800X2 came out. I don't want to say the front fans are critical as much as keeping the drives cool is critical but they are an excellent way of doing so. Semantics I know. As for that R3....well I wish you hadn't turned me on to that....I'm going to have to look into that. Turns out Newegg actually sell them and at ~$110 it looks positively drool-worthy.
Of course after all that, you could also take a look at one of these:
http://h10010.www1.hp.com/wwpc/us/en/sm/WF05a/15351-15351-4237916-4237918-4237917-4248009.html
http://forums.freenas.org/showthread.php?32-Freenas-8-on-Hp-Microsvr-Nl361
http://hardforum.com/showthread.php?t=1555868
-Will