It's an 8 virtual CPU server. Four physical CPUs. I'd heard the same thing about hyperthreading not offering much of a speed bump, but since we plan on leaving HT turned on while it's folding (it won't be doing anything else so other applications won't matter) it still seems like there should be a recommended way of configuring it. Either starting the four folding processes and let them share all the CPUs, or if the affinity should be set so each folding process has a physical CPU all to itself (which is what is recommended for multi CPU machines I think).
For setting up affinity you are given virtual CPU 0-7. I've never found anything that tells you how those CPUs correspond to the actual physical CPUs and without that there is no way to know how to give each folding process it's own physical CPU. In other words, is it CPU 0 and 1, then 2 and 3, etc. that correspond to a physical CPU, or is it CPU 0 and 4, and 1 and 5, etc. On a machine with 4 or less virtual CPUs it doesn't matter of course, just assign each folding process to one of the virtual CPUs.
In my head I calculated that having five 4-way servers folding for 3 weeks is worth over a years worth of processing on a single CPU machine, so a little tweak here or there could be worth some serious beans!

Maybe I'll try the Stanford F@H forum and see if anyone over there has heard of recommendations.