I've seen arguments for and against this but do you personally use the no follow tag on affiliate links? Does google have any reason to penalize a site with affiliate links? I can understand if its a few pages all stuffed with links, but my site has thousands of pages and I'm only just making a sort of store front with aff links on it.
I nofollow affiliate links whenever I can. It's not so much to protect myself from a Google penalty (they can see it's an affiliate link whether I nofollow or not), but to give more weight to the other links on my page. If you're linking to other sites that you own or other pages on your own site, those links will carry more juice (if I understand the process correctly) if there are fewer links on the page. As I understand it, most search algorithms consider a nofollow link to be the same as no link, and therefore it doesn't dilute your other links.
Thanks for the reply, that was my line of thinking but then on some other forums people ask the question "why would you want to tell google that you don't trust your affiliate, if it's relevant then don't nofollow" now I'm paranoid.