First off… Before you go changing all your links – make sure that the reason you are being ‘banned’ or ‘penalized’ is the affiliate links.
I have severe doubts that any of the search engines penalize for this… After all, the majority of websites out there are affiliate sites with afflinks in plain view. Some of them (in other industries) have PR7-8! What does that say??
One of my sites, I had thought was penalized in Yahoo for Affiliate Links. I, however, had some common content which was on ALL my pages. I created new content for each page and was re-listed on Yahoo within 1 week. (WITH affiliate links showing).
Do your homework…
kw