Do Com Junct links affect your site with Google and Penguin

[Statrak]

We received the dreaded letter from google in reference to "unnatural or artificial links" Our site has affiliate programs through Commission Junction and Link Share and between the two programs we have over 8000 affiliates or advertisers. Our site has been very successful, but our organic search traffic is down as our rankings in the search engines have dropped. My question is do the affiliate links have an effect on our site with Panda or Penguin?

[MichaelC-15022]

Penguin:  those links aren't your problem.  As Matt states in this video, they're already handling all of the major affiliate programs automatically (and in most cases, you'll see the affiliate program implemented as non-301 redirects anyway).

Panda:  Panda is not a link-based measurement--it's a measurement of site quality based on on-page content, layout, etc.  You're talking about inbound links from your affiliates, through an affiliate program, TO your site....so not an issue.  Having said that, if on YOUR site you had a ton of OUTBOUND links that was occupying a lot of the above-the-fold real estate on your pages, now that COULD affect how Panda sees your site (in a negative way).