What do search engines think of them?

Just that pages with a lot on seem to have lower PR than pages without, do search engines penalise pages with a lot of affiliate links on?

Ive just made a redirection script which I am abouts to put in place so that there arn't any affiliate links on my pages, but theres a whole lot of links on a whole load of pages..... so is it worth it?

Edit: Poor typing