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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).