n00b1 - 1:49 pm on Aug 15, 2011 (gmt 0)
Everyone will probably have a different opinion on this but I have had some experience on my own site that would suggest that adding the 'nofollow' attribute to affiliate links can actually do harm to your rankings in a post-panda universe.
My own website took a bit of a dive (not a catastrophic one) after Google's 'Panda' update. This followed a massive overhaul of the website before that (for the new year) which was, ironically, designed around the kind of things Panda is supposedly looking at - creating a more engaging user experience, better content etc... So I didn't want to dive in and make any sweeping changes because frankly, I could see no reason to do so (especially given that others many others were basically dismantling their websites and seeing no good come from it). One thing I did do, however, is remove the nofollow attribute from all of my affiliate links. Around a week later (possible coincidence but not in my mind) the website rose again in the rank for all of its key terms and enjoyed some positions it hadn't enjoyed even before Panda.
My personal take on this - if you are affiliated with a 'trustable' source there is no reason to try to hide anything from Google and they actually dislike you doing so.