My pentium D 940 @ 3.6 ghz made 1034 points per day folding@home. My Q6600 @ 3.6 makes 3250 ppd. So twice the cores makes over 3x more points.
A Q6600 can be had for $270, and a pentium D 925 for $50. So 5x the price for 3x the points; now its getting a bit more interesting.
I would go for the $99 Gigabyte board
http://www.newegg.com/Product/Product.aspx?Item=N82E16813128059
with a $50, P4 925 overclocked to 3.6 ghz
http://www.tigerdirect.com/applications/SearchTools/item-details.asp?EdpNo=2525999
using a thermalright $35 heatsink,
http://www.newegg.com/Product/ProductList.aspx?Submit=ENE&DEPA=0&Description=xp-90
you need the adpater below the heatsink listed.
That makes your build $190 with a dual core and great performance for the price. I use that same heatsink on a quad with good results so it can be used to upgrade later if you went to a quad. The mobo overclocks well and the CPU is dirt cheap.