SMP folding really doesn't like it when you have else something loading the CPU - even 10% load on one core can halve your PPD - I remember my HTPC's PPD dropped all the way from 3500 to 41 because Media Center got into an infinite loop and clogged up one of the 4 cores.
If you have a strong CPU like 2500k or 2600k, do not fold an AMD card with it because the CPU alone will net you more points than CPU+GPU because of stolen CPU cycles from the GPU client. If you do decide to fold on ATI, make sure to use the Version 7 folding client so you get the newer work units.
"The computer programmer says they should drive the car around the block and see if the tire fixes itself." [src]