It really depends what you are trying to do. For most games, the limiting factor is the graphics card, so in most situations the build with the stronger graphics card will give the highest performance (as long as the processor is solid).
The flipside of this is that the GTX760 is perfectly capable of running most games more or less maxxed out, at common display resolutions. If you are resolution limited then you aren't going to notice any tangible performance boost from spending extra on graphics, bar a bigger performance buffer as games become more demanding.
Some general thoughts about both builds-
I don't know if the Hyper 212 Evo is compatible with the Gigabyte Z87-N because it has a slightly awkward CPU socket positioning. It's worth trying to find this out. For this reason, I'm not a huge fan of this motherboard as it's a bit limiting.
There is no reason not to go for 1600Mhz (or more) memory. In the Z87 build, you could probably justify the extra spend to 1866Mhz+, though H87 is limited to 1600Mhz. In both cases, it shouldn't cost you much extra and is definitely advisable.
A 500Gb HDD doesn't make a huge amount of sense right now, as often 1Tb drives are very close in price. In this case you can pick up a 1Tb Barracuda or Caviar Blue for $60 which is far better value for money.
In most ITX cases, a reference blower cooler makes infinite sense, but the Prodigy has pretty great airflow and doesn't really need the exhaust in the same way many smaller cases might. If you want to stick to EVGA, then the models with the ACX cooler will probably offer better performance at a similar price. If you are open to brand change, then there are compelling options from MSI, Gigabyte and Asus within a $5-10 price range on both the GTX760 and GTX770.