Help on a $500 build, using the bitfenix prodigy

The case is the thing that is holding you back, in terms of performance.

AceofDiamonds has the right idea in that his build you can upgrade the CPU+graphics card, it's hard to do better for the price.

The best machine you can build for $500 is significantly better than that though, ITX motherboards are more expensive than their mATX versions, and the case is quite expensive too.
For the same price you should be able to get a solid quad core and something like a HD7870. It's the case that holds you back.

The case price jumped back up $30 bucks. Anyways, the first upgrade I suggest is the CPU. You can upgrade to any Ivy bridge lga 1155 CPU like a Core i5 3570k. Then you can go for a better GPU like a radeon 7870 or 7950 or gtx 760. Make sure you check to see if these things can fit in your case.

The Bitfenix Prodigy isn't that small (I have two). It's very wide for a "small" case, and you need extra clearance(s) to accommodate things like the I/O panel on the side.
Another point that hasn't been addressed is Wifi. If you want it, it'll cost you, as you need to include it in the motherboard specs (no room for a PCIe card).

You are looking at something like this for best value $500 -
PCPartPicker part list / Price breakdown by merchant / Benchmarks

CPU: AMD FX-6300 3.5GHz 6-Core Processor ($109.99 @ Newegg)
Motherboard: Gigabyte GA-970A-D3P ATX AM3+/AM3 Motherboard ($54.99 @ Newegg)
Memory: G.Skill Ripjaws Series 8GB (2 x 4GB) DDR3-1600 Memory ($49.99 @ Newegg)
Storage: Seagate Barracuda 1TB 3.5" 7200RPM Internal Hard Drive ($58.13 @ OutletPC)
Video Card: Sapphire Radeon HD 7870 GHz Edition 2GB Video Card ($160.66 @ Newegg)
Case: Antec One ATX Mid Tower Case ($29.99 @ Newegg)
Power Supply: Corsair CX 500W 80+ Bronze Certified Semi-Modular ATX Power Supply ($39.99 @ Newegg)
Total: $493.74
(Prices include shipping, taxes, and discounts when available.)
(Generated by PCPartPicker 2013-12-05 22:58 EST-0500)
Dramatically better CPU and a decent GPU upgrade over Ace's build. You could go with FM2 platform and the X4 750/760, but you don't save much over the AM3+, and it's not as flexible.



The 3570k requires a Z77 motherboard and a CPU cooler to utilize it's value, which is more expense.
To illustrate the point -
THIS BUILD IS NOT A RECOMMENDATION
PCPartPicker part list / Price breakdown by merchant / Benchmarks

CPU: Intel Core i5-3570K 3.4GHz Quad-Core Processor ($214.96 @ SuperBiiz)
CPU Cooler: Cooler Master Hyper 212 EVO 82.9 CFM Sleeve Bearing CPU Cooler ($29.26 @ OutletPC)
Motherboard: MSI Z77IA-E53 Mini ITX LGA1155 Motherboard ($109.98 @ SuperBiiz)
Memory: G.Skill Ripjaws Series 8GB (2 x 4GB) DDR3-1600 Memory ($49.99 @ Newegg)
Storage: Seagate Barracuda 1TB 3.5" 7200RPM Internal Hard Drive ($58.13 @ OutletPC)
Case: BitFenix Prodigy (Orange) Mini ITX Tower Case ($79.99 @ NCIX US)
Power Supply: Corsair CX 500W 80+ Bronze Certified Semi-Modular ATX Power Supply ($39.99 @ Newegg)
Total: $582.30
(Prices include shipping, taxes, and discounts when available.)
(Generated by PCPartPicker 2013-12-05 23:07 EST-0500)
That's about as cheap as you can make a 3570k in a Prodigy, it doesn't even have a graphics card included and it's already $80 over budget. Add in a sensibly balanced graphics card, and you are looking at more like an $800 build than a $500.

The first build I linked you isn't huge, but it's a standard PC tower. You can attempt to shrink it by going to the mATX format, but it really isn't worth it as AMD builds just don't work at smaller form factors. If you attempt to transition to Intel, you end up back where you started but with an extra $60 or so to play with from savings on the case and motherboard. Here's the best I can do-
PCPartPicker part list / Price breakdown by merchant / Benchmarks

CPU: Intel Core i3-3240 3.4GHz Dual-Core Processor ($120.98 @ Newegg)
Motherboard: ECS B75H2-M3(1.0) Micro ATX LGA1155 Motherboard ($48.98 @ Newegg)
Memory: G.Skill Ripjaws Series 8GB (2 x 4GB) DDR3-1600 Memory ($49.99 @ Newegg)
Storage: Seagate Barracuda 1TB 3.5" 7200RPM Internal Hard Drive ($58.13 @ OutletPC)
Video Card: Sapphire Radeon HD 7870 GHz Edition 2GB Video Card ($160.66 @ Newegg)
Case: Fractal Design Core 1000 USB 3.0 MicroATX Mid Tower Case ($29.99 @ Newegg)
Power Supply: Corsair CX 500W 80+ Bronze Certified Semi-Modular ATX Power Supply ($39.99 @ Newegg)
Total: $495.72
(Prices include shipping, taxes, and discounts when available.)
(Generated by PCPartPicker 2013-12-05 23:16 EST-0500)
It should perform fairly similarly to the AMD build, and it's a bit smaller, but I can't honestly say it is a good choice.