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I recently had one of my personal affiliate sites drop from the SERPs. It's relatively new so it's hard to tell if it's been sandboxed or penalised but I have done some things to correct this.
The reason for your site dropping is almost certainly because it was perceived as a 'thin' affiliate site. i.e. low quality/duplicate content that was geared towards squeezing people through affiliate links. Google is coming down on these guys harder than ever - I wrote my own content based on research, but my possible problem was that there were only 10-15 pages at the time.
Since then I have quadrupled the content and the reason I didn't switch sites is because I had an exact match domain that I didn't want to lose. I would say, in your case, start again - get all your content indexed first without affiliate links and then add them to places that you see are most appropriate.
Don't just throw affiliate links everywhere, the links work far better in some spots than others; take your time to add them and be careful not to go overboard.
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Agreed this is a VERY "thin" affiliate site - not just dupe content but really redundant, keyword-stuffed content besides. Not good!
In my experience, it's not the size of the site or the amount of the content so much as the ratio of good content to everything else. Make the home page less promotional, don't overdo keyword density and be selective about where you place the ads. Improve the quality of the content overall. I see a lot of repeated text in your page titles - make your page titles more unique from page to page.
Do that and make sure you're OK as far as Google's other webmaster quality guidelines. If that doesn't bring it back in several weeks, then try a reconsideration request.