NOPE!
On a single processor system you end up with both applications fighting for the unused CPU cycles and in the end you have two apps with neither one of them running efficently. I have actually heard people report that SETI @ Home is a bit more successful at grabbing cycles so the Folding @ Home app. really takes the major performance hit.
On a dual processor machine it should be possible to run one app on each processor and only experience the normal performance hit one experiences due to the system overhead that is normal with a dual processor setup.
The better alternative if you wish to support both projects is to run either one on the machine for some time period(a week, a month, etc.), then switch to the other and run it an equal amount of time.
SkyHook