This interview with Vijay Pande, one of the gentlemen behind Folding@Home, is getting kind of old but there are a couple of points worth pointing out. Mainly concerning running Folding@Home on the PS3 -- some people have been running "stress tests" to see how Sony's console can handle the program over extended periods. Those people can stop, because they'll be doing that forever. In any case, the PS3-specific questions were answered by SCEA 's Richard Marks (who's doing a stress test himself). Let's list it up!
Is it safe to leave the PS3 folding for 24/7?
Yes. There's no indication that the PS3 has problems over long periods of folding... but of course, you should ventilate the darn thing so it won't overheat.
Well... should people give the PS3 a break to cool off?
No. It shouldn't need a cooling period. You know that whirring thing? It's a fan. It regulates the internal temperature. [note: PS3Fanboy added some "attitude" to this response, because we like attitude]
What's stressed the most and will it affect the stability of the PS3?
The Cell processor. Luckily, it's a high-performance processor built for things just like this. Folding@Home shouldn't have any adverse affects on the PlayStation 3's stability.
That's all that we think pertains to running the program on your PS3. Don't worry, guys! Your system is completely safe and that's a good thing. Waiting for those warranty replacements or whatever aren't the best... plus you only get a refurbished system (read: previously broken) instead of a new one.