So it turns out points are scored based on project, with just a small margin attributed to speed. I like that.
In any case, I've turned to GPU folding and am getting around 1400 points per work unit. Each WU takes around 2:40 to complete, so I'm estimating a PPD of 12,600. Will keep folding with the GPU for a week. Then I'll turn back to the more modest CPU folding; My GPU fan runs at 40% when folding (temps are fine at around 58c) and although not too loud, it still is a big nagging. I adore silence.
I'm amazed at the processing capacity of GPUs. One has to see it to believe it. DirectCompute and OpenCL are awesome technologies that no doubt one day will be properly tapped by applications that require this kind of computation.