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The SE's don't like duplicate content. More specifically they don't want five of the top ten search results offering the same sorts of pages with essentially the same set of affiliate links (or very nearly the same). One can envision literally thousands of categories where this might be the case, even more so since the advent of easily managed aff feeds.
So, the SE's make every effort to identify pages that are unique and useful, however they do that. IF they see lots of pages from different sites that seem to share the same sets of affiliate links, and if the main point of those pages is only to offer up those affiliate links, then would anyone really expect the SE's to want to show all of those pages ranking high in the SERP's.
Only difference now versus several years ago, is that they've gotten increasingly good at weeding out those kinds of pages. When you look at if from the SE's point of view, it's not that surprising or complicated, really. ;-)
The most useful info I can give you is:
1. Don't put more code on a page than you have text.
2. Be as specific about the product as possible.
3. Build 1 page on your site that goes to the advertiser, and send all your links to this page. That way when the advertiser drops out of CJ you won't be stuck cleaning up a bunch of code.
For me, Google + Commission Junction = $$$
Do I use affiliate links with CJ, knowing that Google will kick my page down in the serps but I might make up for it with a few $$$ from CJ, or do I forget the affiliate link and just link directly to the widget, hoping to make up any lost affiliate revenue from CJ with increased adsense revenue because of better SERP visibility?
Maybe a trial is in order... :)
If I were you, I would hide my cj links if possible. You can use redirect scripts to do it. Search engines, no matter what they might say, HATE affiliates.
I haven't seen any evidence that Google hates affiliate links per se. Affiliate sites? Maybe, or maybe not. Boilerplate affiliate pages? Definitely. GoogleGuy made that very clear a while back with his comments about the need for affiliates to add value.
For what it's worth, I used to have CJ links on every page, and now I've got them on just a few pages, but I've never had any reason to believe that Google cared either way.
The further the Slider Button is moved to the left, the less likely it is that the page/site will do well in the SERP's, with the usual caveats of course.