Heres the deal with folding@home, as I see it.
Whichever processor you are using, it will immediately pull back production in order to let you use your programs. It will only use spare clock cycles, and have no performance impact whatsoever. A graph I saw showed that it didnt affect 3DMark03 scores at all.
Now...
On a P4 processor with HT, it doesnt even feel like the program is there, since it will only use 50% cpu while still having same output as an AMD of similar value.
On AMD processors, I would notice a slight hang when beginning to use my computer since it would be using 100% before noticing I was trying to do something. No performance impact in the programs, just a slight hang while opening the programs sometimes.