My dad's extremely high-end build request.

[Cyrops]

Budget 3.5kUSD+
Resolution Haven't clarified but likely tri 1920x1080
Games / Settings Desired He doesn't play much games, he already has a server he has been using for years for running a domain/network controller and mass media space.
Any other intensive software or special things you do (Frequent video encoding, 3D modeling, etc) Video encoding
Country U.S.
Parts that can be reused Nothing but one monitor and a few HDDs
Do you need an OS? No
Do you need peripherals (e.g. monitor, mouse, keyboard, speakers, etc)? Some cheap keyboard, probably not mechanical.

Just in general he's used his server in the past as testing grounds for things he needs to do at work, he works as a network administrator so he can't really afford to mess up at his job.

I'm sorry you say he has money and still plans to use 1080p? Does he know about 1440p?
I'm sorry I tried, but that budget is too small for my "dream" PC:

PCPartPicker part list / Price breakdown by merchant / Benchmarks

CPU: Intel Core i7-4930K 3.4GHz 6-Core Processor ($549.99 @ Newegg)
CPU Cooler: Corsair H100i 77.0 CFM Liquid CPU Cooler ($89.99 @ NCIX US)
Motherboard: Asus Sabertooth X79 ATX LGA2011 Motherboard ($314.99 @ Amazon)
Memory: Corsair Vengeance 16GB (2 x 8GB) DDR3-2133 Memory ($202.68 @ NCIX US)
Storage: Mushkin 240GB PCI-E Solid State Disk ($327.98 @ Newegg)
Storage: Samsung Product Series:840 Pro 512GB 2.5" Solid State Disk ($426.94 @ Adorama)
Storage: Samsung Product Series:840 Pro 512GB 2.5" Solid State Disk ($426.94 @ Adorama)
Video Card: Gigabyte GeForce GTX 780 Ti 3GB Video Card (2-Way SLI) ($724.99 @ Amazon)
Video Card: Gigabyte GeForce GTX 780 Ti 3GB Video Card (2-Way SLI) ($724.99 @ Amazon)
Power Supply: Antec High Current Pro 850W 80+ Gold Certified Semi-Modular ATX Power Supply ($173.98 @ SuperBiiz)
Total: $3963.47
(Prices include shipping, taxes, and discounts when available.)
(Generated by PCPartPicker 2014-02-12 13:53 EST-0500)

It's what I would get, and a tripple 1440p monitors would be another 1.5k-3k.
PCI-E for OS+misc and two SATA's SSD's for RAID.

[ocis]

Well if you want the cream of the crop you can also add a 4K monitor with g-sync to that when they come out

[Remilia]

Well if you want the cream of the crop you can also add a 4K monitor with g-sync to that when they come out

That thing will probably cost half the budget.

[ocis]

Well, for a good one it would cost the entire budget pretty much but that's the catch-22. If you're not going for 4K there's absolutely no real reason to want a $3500-$4000 gaming PC, but then if you are going for 4K then you'd absolutely need one.