At this point in time, GPUs are looking to be the future of the project. With the new GPU core (core 17), a $330 card like the GTX 770 can earn 100k PPD with a reasonable OC, while a similarly-priced CPU such as the 3770k or 4770k is probably only going to earn 20k PPD at best with a decent OC. There have been some issues with core 17 project availability in the last few weeks, but long-term it's going to be the standard and the old GPU cores will be phased out.
You definitely want to get a solid, reliable power supply as well. If your power bills aren't too high, then getting a super-efficient PSU may not be worth it, though at this point it seems like 80+ Bronze is sort of the baseline for most decent units. Everyone probably has a different list of reputable PSU manufacturers; my list would include Antec, Corsair, Seasonic, and EVGA, but there are several others that I've heard good things about as well.
Other things like RAM, hard drive, etc., aren't worth putting much money into for a dedicated folding box, as they don't affect performance enough. Some people actually skip a hard drive altogether and run Linux off of a flash drive. Most popular distros don't require much space; I think an 8 GB drive would be enough room for a Ubuntu installation. At worst you'd bump up to a 16 gig drive. Any old hard drive lying around would also work; there's not much of a benefit to FAH going from a mechanical drive to flash memory. With RAM, 4 GB of DDR3-1600 should be fine. Faster RAM will slightly improve CPU performance, but not enough to be worth the price increase.
My suggestion would probably be the 770 I mentioned above, plus shopping around for the other parts. I believe a 760 or 670 do around 70k PPD, so while that makes it easier on the budget, you'd be taking a notable performance hit. The 780 is one of the best value buys, but at $500 for the card alone, it may be outside your budget when factoring in the other components. Both of mine OC'ed to around 1215 MHz hit between 170-220k PPD on core 17 projects (and in some cases, it depends on which run of a certain project they're working on).
I'm not as familiar with the AMD side of things, and it seems like lately folders have been avoiding them for dedicated builds because of the price inflation due to their mining prowess. I think at their original price points their folding performance levels matched up with their comparably-priced Nvidia models, but they're not as desirable with that crypto markup.