From my seat of the pants feelings.... being I am starting to think about the upgrade thing.
If you want to fold or folding is more than a fancy.. forget amd gpu's their points suck. ppd/$ is too low. Unless some new clients have improved the situation you will get 1/4 the points for equal money.
Dual core/quad core. from my folding farmer perspective, the money is in gpu clients, and money spent anywhere else is wasted. And since the cheapest quad core is
$139.99 and the cheapest dual core is
$59.... quad is out, because the additional $80 will buy me an
nvidia gpu worth 6k/day, that I can plug in on a dual core MB at no additional cost. However for a general use machine, the Quad/gpu combo would be much better and more responsive to any other work you wanted to do.
My current machines running one instance gpu on a dual core machine are waaay slower than they were with just smp running, and there is more than just a few video "oddities" that crop up, but they are still usable for some 3d work and surfing.... with two gpu instances, I am not sure I could even surf the web...., and I have not tried two gpu instances with two cards on any of my machines. gpu/smp/winxp has been a no go for me.
XP/Vista.... No Idea, All I have is XP. Vista, from what I read, is better at the gpu/smp combo.