Starbuck13

There are tons of options.  You don't even have to go dual CPU (even though the system can handle 4x XEON 8-core CPUs ).  the 810 IS 2.5" drives, but they have several other machines that can handle 8, 16, 24+ 3.5" drives.  That was just the first thing I grabbed on a quick browse.  That's also a rackmount unit.  They do have workstations, too, that can handle quite the number of drives on the cheap.  You'd also be surprised at how quiet some of them can be, especially, if you decide to use your own cooling solution.  
 
EDIT: Here's a Tower, and these can be set to run pretty silent, and have good space for custom cooling solutions.
$1090.00

Dell PowerEdge T710
2x XEON 2.66 Hex core X5650
Memory 64GB PC3-10600R
SAS 6/iR RAID Controller
Dual Gigabit Ethernet NICs
1100W PSU
 

Just checked Servermonkey.com and viewed the following configuration for a 2U rack option:
$1055.00 - USD

Dell R810 6-port
CPU - 2x Xeon Hex core 2.0GHz E7540
Memory - 64GB PC3-10600R  (16x4GB)
RAID - SAS 6/iR RAID Controller Card
Remote - iDRAC6 Express Remote Access Card
Network - 4x Gigabit NICs
PSU - 1100W 
 
Supports 6x 2.5" Drives

Water cooling would be totally unnecessary, add a bunch more hassle, and is generally less reliable than air cooling. Water cooling it doesn't really make sense. I'd go for a noctua NH-D14, and since the chip is very low power, the fans will not need to spin very quickly. The noise level can then be further reduced with a custom fan speed curve. Freenas along with ZFS is a very solid option, and is highly proven at this point. I run FreeNas 10 on my server, and am very pleased with the functionality. 
 
How many plex streams are you hoping to run from this machine? I think it should be able to transcode 3-ish videos simultaneously. 
 
Have you looked into second hand options? Old pre-built server gear tends to be horribly loud, and absolute power hogs, but you might be able to find something that fits your needs at a reasonable price. 

Have you considered lightly used setups?  Some people forget that older server setups are quite powerful for consumer use and fairly inexpensive.  I often go to places like servermonkey.com and build out monster setups for under $2000 that are beasts in storage capacity and computing power.  It's not unheard of to find a 2x Xeon quad or hex core server with 64GB registered memory and numerous storage bays, on the cheap.  You can find these super deals on Amazon and eBay too.

The Noctua looks good, though it's too large for my 2U chassis. The NH-L12 looks good, though.  Very glad to hear FreeNAS is working well for you. I've heard about it here and there, but this is the first time I've actually looked at using it myself, so I was a little hesitant. ZFS is a huge selling point for me there, as well.
 
3 streams would probably be higher than average usage, so that's right in the sweet spot of what I'm looking to be able to do.
 
I have looked a little bit at older server gear, but the power consumption has been the killer there so far. I'll keep poking around though and see what comes up. I've got plenty of time to save up for this.

Arctive Alpine tend to be all aluminum heatsinks.  For Passive thermals, I like to use copper or copper pipe to aluminum rad.  

Thanks for the tip. I've swapped out the Arctic heatsink for a Dynatron K618, which ought to do a better job.

Very good choice... and taste.  I think you'll like that cooler a lot and find impressive thermals.

Its bad. Id probably just the storage spaces in windows, its better than mobo raid.
 
If you want a card to run hardware raid, either get something like a used dell h700 or a lsi 9361 8i. Cheap raid cards aren't worth it. Id suggest storage spaces for your use.

That PSU is good and you have the money in your budget for the 1080 and if you plan for 4k then the 1080 will be the better card for it.

The i7 is not a huge increase over the i5. It doesn't make much difference in gaming. It's main thing is that it has Hyperthreading and can handle 8 threads.
If you plan to use this system as a media server, and other people may be accessing media will you are using the computer, the extra threads of an i7 might help.
Also, if you do any video editing, etc, the i7 will make encoding, etc, faster.
 
It's up to you if the i7 is worth the extra money or not.