If you're paying for power, go 4P with the AMD Opteron 61xx that has the most cores that you can get. The newer versions are getting close to the 61xx series as far as folding performance, but for the $$, they are still the best bet (last time i checked). The entire rig should pull from 500-800 Watts or so depending on setup. Look over at [H] (HardForum
) for most of the best information on 4P rigs. $3k - $5k on the rig should get you around 300k-800k PPD.
If you're not paying for power, look into the Radeon R9 290X or 7970 (as well as the nVidia 780 (Ti); maybe some 690 action?) The 780 just dropped $150 in price, so they are likely a pretty good deal. The Ti should be around $50-80+ of a premium on that, I'd guess. The new high-end GPUs should pull around 300-350 Watts each and the rest of your rig will likely pull around a max of 200 Watts. Looks like the 780s are getting in the neighborhood of 150k-180k PPD each (netting around 500k-600k PPD total with a CPU).
If money is no object, go with a 4P Intel setup if you can actually afford it, but an Intel 2P setup would be great too (two Xeon E5-2660 v2 look good - 10 core/20 threads each). Throw in some nice GPUs and you have a good monster too!