PCPartPicker part list:
http://pcpartpicker.com/p/Mg2xMp
Price breakdown by merchant: http://pcpartpicker.com/p/Mg2xMp/by_merchant/
CPU: Intel Xeon E3-1231 V3 3.4GHz Quad-Core Processor ($237.99 @ SuperBiiz)
CPU Cooler: Cooler Master Hyper 212 EVO 82.9 CFM Sleeve Bearing CPU Cooler ($25.98 @ OutletPC)
Motherboard: ASRock H97M Anniversary Micro ATX LGA1150 Motherboard ($51.98 @ Newegg)
Memory: Crucial Ballistix Sport 16GB (2 x 8GB) DDR3-1600 Memory ($82.67 @ Amazon)
Storage: Crucial BX100 250GB 2.5" Solid State Drive ($78.99 @ SuperBiiz)
Storage: Seagate Barracuda 1TB 3.5" 7200RPM Internal Hard Drive ($43.99 @ SuperBiiz)
Video Card: EVGA GeForce GTX 750 Ti 2GB FTW ACX Video Card ($136.99 @ SuperBiiz)
Case: Phanteks Enthoo Pro ATX Full Tower Case ($99.99 @ Amazon)
Power Supply: SeaSonic 450W 80+ Gold Certified ATX Power Supply ($73.98 @ Newegg)
Operating System: Microsoft Windows 10 Pro OEM (64-bit) ($134.99 @ SuperBiiz)
Fan Controller: NZXT Sentry Mix 2 Fan Controller ($24.99 @ SuperBiiz)
Total: $992.54
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2015-08-10 00:19 EDT-0400
I changed a few other things as well
The case because the enthoo pro is equal to the 780t and it is cheaper If you must spend that much get the enthoo luxe, again, why so much budget for a case?
https://www.youtube.com/watch?v=cBhmn21ylkc enthoo pro review
https://www.youtube.com/watch?v=IihNgyt-ztE 780t review
https://www.youtube.com/watch?v=cQOPK-OgvnM enthoo luxe
This RAM has a lower CAS latency and it is low profile
The xeon only really needs a 212 evo to cool it
This motherboard is basically equivalent for your needs, and it is not cheap quality, it is just a REALLY good deal right now.
This PSU is worlds better and will be fine with long workloads.
Dont plan on doing amazing gaming on this thing
Just out of curiosity. What game server are you running?