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Also, back in 2006 and early 2007 when google policy against buying/selling links was not very strict, i had purchased some links from webdirectories and few blog posts from some blogs and may be some other cheap link building service (i was totally unaware of google's link buying/selling policies). My question is, should i try to get all those links removed as well? those links are pretty old by now and probably add no value to my site but it might be hard to first approach the owners of sites and then get them to remove my links and blog posts. I would like to see what the experts have to suggest on this. I can share my case study as well.
I think if you can justify those affiliate links as being relevant to the on-page content and useful to your users, as per the Google guidelines, then maybe it's time to look at other possible reasons for your penalty. Agree with Tedster though, try the nofollow.
Prudence: I have injected thousands of words worth of articles ever since i got penalty and none of that unique content helped.
Those links are relevant, however, one year of testing has lead me to believe that they are the ones which are causing me harm. Also try to reduce on page optimization and see if that helps e.g reduce excessive usage of keywords?