I agree, maybe $350 tops. Depreciation on tech is pretty bad, just like cars (if not worse). Being custom built has little to no value unless it's custom built for whoever is buying it. There's not really much 'custom' about putting together pc parts. That would more apply to some sort of case modding like a professional airbrush job, custom water cooling loop with things like hardline acrylic tubing bent and setup by hand to achieve a really unique look and then custom stuff is hard to resell sometimes.
Take a car or motorcycle with a fancy high dollar airbrush job. Maybe it looks beautiful and the original owner loved it but maybe not everyone wants a mural of Merlin casting lightning from his magical staff all across their hood. I doubt it will bring anywhere close to what you paid for it. If someone were extremely careful with their budget they could build an i5 based machine for $600 new. Figure $25 for the ram, $25 for the used hard drive (being generous), $100 for the gpu and $100 for the cpu, you're looking at $250. 8gb of ram new, $60. 1tb hdd new, $50. Brand new i3 @ 3.6ghz, $110. Brand new 7770 2gb, $120. I stand corrected, those same components new would only cost $340. If selling just those parts, no case or psu with it, maybe $250. $300 tops if it included the case and power supply.
Depending what motherboard you have, you might be able to keep it and upgrade the cpu and gpu. Also depends what power supply and what wattage it is. You could keep the hdd and the ram. Even if you had to upgrade the cpu, mobo, graphics card and power supply - keep the ram, case (provided the gpu fits) and hdd, for around $570 you could do something like this.
PCPartPicker part list /
Price breakdown by merchant
CPU: Intel Core i5-4590 3.3GHz Quad-Core Processor ($193.99 @ SuperBiiz)
Motherboard: ASRock Fatal1ty Z97 Killer ATX LGA1150 Motherboard ($90.98 @ Newegg)
Video Card: Sapphire Radeon R9 280X 3GB Tri-X Video Card ($219.99 @ Newegg)
Power Supply: Antec HCG M 750W 80+ Bronze Certified Semi-Modular ATX Power Supply ($64.99 @ Newegg)
Total: $569.95
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2015-03-21 12:48 EDT-0400
Note: the z97 motherboard isn't necessary for a locked cpu with a single graphics card, however if it had to be upgraded it gives the option of an unlocked k series cpu in the future if you thought you might do that. Say in 18mo or so you wanted a k series i7, you wouldn't have much luck with an h97 board and would be back in the same pickle needing a hefty upgrade.