Home server build

I am working on replacing my aging home server and was hoping to get a little advice on the hardware. The server will be used as a cqc server, nas, for backup, a plex server and a tv recording backend. I am likely going to run WHS2011 but have not completely made up my mind yet.
 
The build list can be found here: https://secure.newegg.com/WishList/MySavedWishDetail.aspx?ID=27304706
 
Any advice is appreciated.

I cannot get to your build list link; even after logging in to NewEgg.  There is a bunch of public wish lists but do not know which one is yours.
 
Over the years here have gone to smaller footprint mITX motherboards in smaller cases.  The larger style motherboards with multiple slots are still very popular as are the larger cases. 
 
Here currently (vivo) building two new servers using the new (well old) 4th generation of Intel I-Series CPUs.  Basic no frills mITX motherboards with HDMI, VGA and DVI video interfaces, USB 3.0, 16Gb of memory.  These are just going to be utilized for automation servers. Prices for the "Haswell Intel" motherboards are all over the place as are the 4th generation Intel I-series CPUs.
 
My currently newest NAS box (old now) is an 8 hot swap 3.5" case with an AMD E-350 (well an AMD equal to an Atom?), A TV recording box called MythTV with 2 onboard tuners and 4 networked tuners (HD HomeRun) using a BCM industrial style mITX board.  Currently running Wintel Server automation boxes are also using the BCM motherboards along with now two ZoneMinder boxes.  I did get a bulk purchase deal on the BCM motherboards.

I thought it was... Here are the components I am not sure of. This motherboard: http://www.newegg.com/Product/Product.aspx?Item=N82E16813132122 Core i5: http://www.newegg.com/Product/Product.aspx?Item=N82E16819116897 RAM: http://www.newegg.com/Product/Product.aspx?Item=N82E16820233388

Good stuff Mike!
 
I was looking a similiar '97 gaming series Haswell mITX motherboard.  Except didn't need the included wirelessstuff.
 
I have looked at all of the same series offered by Gigabyte, Asus, IRock, et al.  They all make them.  The newer 5th generation I-Series is just starting to sell.  It's difficult to keep up with the technology.  Thinking the current BCM boards I use are also sold by Micron.
 
Are you looking at a 4-drive or 2-drive NAS?  What kind of box?
 
Last NAS box here used a updated firmware IBM M1015 6 port SATA3 Raid card updated to current LSI firmware.  Initially the Asus E350 bios did not recognize the LSI card; a month later an updated BIOS did work.  The card is a bit big with many passive heat sinks on it that do get a bit warm.
 
A neat forum for DIY building your new home server is called "Serve the Home" dot com.  Lots of server obi wans there.
 
Here splitting it out to two case styles.  One tiny mini-pc no frills case (tack on the wall type - DIN style) and one a bit larger with a multimedia home box look to it.
 

 
 
 
Today just utilize mini-pc box (Aopen Digital Engines) for my XBMC boxes which sit next to the televisions.  These are very quiet and have a tiny footprint.
 
I am assuming you are installing the box next to the television eh? 

I am going to use a 5 in 3 hot swap cage for the drives. 5 hard drives for storage using flexraid, an ssd boot drive and two blu ray burners. I am told that my norco server has to come out of the extra bedroom so this will replace that and go in the entertainment center. 

I've purchased a number of i5's, and have tried to compare apples to apples between the i5 and i7 cores, but the i5's were always around $100 cheaper when comparing roughly the same clock speed. I was late to the party a couple of years ago when I realized the benefit of HyperThreading with i7's. Wiki can do a much better job of explaining than I can, but I'll provide a couple of screen shots anyway:
 
Core2Quad:

 
Quad Core i5:

 
Quad Core i7 w/o HyperThreading:

 
Quad Core i7 w/ HyperThreading:

 
The latter is my latest server build which I am looking to use to virtualize a few of things...

I have been torn about going all out with an I7 or sticking with the i5 it is going to be on 24/7 so I'm trying to be reasonable and keep power use down. That being said I'll probably end up running a couple vms...

Yeah here in my two builds comparing a purely Linux box to a Wintel box; still mostly single purpose though. 
 
5th Generation I-Series CPUs (Broadwell) are nice and will be driving the 4th generation I-Series CPU prices lower.
 

I am going to use a 5 in 3 hot swap cage for the drives. 5 hard drives for storage using flexraid

Click to expand...

Yup the 8 drive case that I used for the NAS box is pure drive hot swap with little space for anything else.  There was only enough spare space in it for the LSI raid card and boot drive.  Its only purpose though is to be a NAS.  It looks OK in the basement cuz I never look at it.  The oldest NAS box is a 1U 4 drive hot swap running embedded Wintel server.  Next one was a custom job with a 3-Ware 4 in 3 drive cage in it.  Its kind of large though.  Rest of them went to Linux / BSD (3 of them).
 

 
Today recorded TV stuff is just kept on the MythTV box.  If I want to save something then keep that on a dedicated multimedia for use only NAS.  XBMC boxes too have some storage (160Mb-1TB) to temporarily keep files there.  (watch and throw away media).  I did play a bit with installing a Plex server concurrent with the MythTV stuff (along with Squeezebox server).  It worked.  I also keep a Wintel server running PlayOnTV which still works fine for me. 

Once I get my server build completed I need to jump back to my NAS (unRAID) solution; I've had a (3) 5.25" to (5) 3.5" hot-swappable drive bay collecting dust for almost a year now...
 
http://www.amazon.com/Supermicro-CSE-M35T-1B-Mobile-Rack-Black/dp/B00009ILU1/ref=sr_1_1?ie=UTF8&qid=1424186204&sr=8-1&keywords=CSE-M35T-1B

Thanks Pete. Any other thoughts on performance vs power usage between i5 and i7?

I'd much prefer to have more computing power with an i7 than to end up strapped with an i5, particularly if you are planning to run multiple VMs. 
 
I can't comment all that much about the power usage; I guess I'd have to ask (someone else) if a i5 @ 50% consumes more power than an i7 @ 35% or whatever the theoretical numbers may end up being. Fortunately I'm not in an expensive power region of the US and I haven't looked into it all that deeply; I currently have a Core2Quad (media server) that runs 24/7, and I never shut off my desktop (i5) PC (it just goes into Sleep mode). I do have a Kill-A-Watt that I could connect to them, but they also do different things so power consumption is going to be different anyway.

Really how much you want to pay for the best bang for the buck (bang==> fast and lower power). 
 
Personally here do not mix my multiple streaming recording stuff (TV or CCTV) with my automation stuff.  Never have with Homeseer.
 
This was in the analog card capture days. 
 
Today I do see folks using VM's and mixing CCTV, TV Capture, Home automation and NAS on boxes.  It works for them.
 
TV capture works better here with HDHomerun for me than the two analog cards in the box.  CCTV from HDIP cams work better than the old analog 8 port capture card stuff.

Yes, my new i7 build is currently planned to have (2) VMs at a minimum; one for my NVR (Blue Iris) and another for my media center (SageTV). Once I get those setup and running I'll have to take a look at how well the CPU is doing under load. I'll end up with (6) 1080p cameras on the NVR and my current STV server has a total of 6 tuners (4 HDHR, and 2 HDPVRs).

I would be interested to see what the power difference between the core2quad and the i5 as that is what I am replacing.

Of all the things you list Plex will be the one needing the most resources and the one it will need most is CPU.  The other things are really insignificant, Win7 needs more resources than the CQC running on it.  I used to run CQC on an 512MB XP VM, now 2G but only because on Win7 and I use multiple RDP sessions.
 
I am currently running a Quadcore i5-3450, running ESXi.  My Plex VM has 2Gb of memory and all 4 vCPUs.   If I stream a native encoded blu-ray to my Roku at the highest level, Plex will saturate all 4 CPUs.  But the best thing about Plex is you can bump down the quality to make it all work.  Lowering the quality a level or two is often unnoticeable.  It is no different then what DirecTV or Netflix do with their "1080p" streams.  And if you are not transcoding there is almost no hit at all to CPU.  It really depends on what files you have and want the client device supports.