Just been reading Matt Cutts: Gadgets, Google, and SEO May 16th post on Indexing Timeline. Here's the tellall part about affiliate sites in his Closing Thoughts.. "..And if you’ve got an affiliate site, it makes sense to think about the amount of value-add that your site provides; you want to provide a reason why users would prefer your site."
Yeah .. I read it too. At least now we know that all the indexed pages filter, and lack of indexed pages, and suplemental ones, were in fact caused by linking to spammy websites.
As far as I can see it's a positive step, owners of affiliate sites will have to make more of an effort to deveop unique/worthwhile content.