Google’s Matt Cutts participated in a keynote discussion at SMX Advanced earlier this month. Among various other topics, Cutts talked briefly about affiliate links with moderator Danny Sullivan.

SMX just uploaded the relevant clip of the discussion to its YouTube channel today, and to reiterate the point Cutts made, fellow Googler John Mueller posted the video to Google+:

John Mueller 5 minutes ago

Regarding affiliate links and "nofollow" – here's what Matt had to say:

"We handle the vast majority of affiliate stuff correctly because if it is a large enough affiliate network we know about it and we handle it on our side. Even though we handle I believe the vast majority of affiliate links appropriately if you are at all worried about it, I would go ahead and just add the nofollow because you might be earning money from that."
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In Google’s quality guidelines (the basis for the Penguin update), affiliate programs come up more than once.

“Avoid ‘doorway’ pages created just for search engines, or other ‘cookie cutter’ approaches such as affiliate programs with little or no original content,” Google says. “If your site participates in an affiliate program, make sure that your site adds value. Provide unique and relevant content that gives users a reason to visit your site first.”

Google has a page about what it means by “little or no original content,” which talks about “thin affiliate sites”. There, Google says, “These sites collect pay-per-click (PPC) revenue by sending visitors to the sites of affiliate programs, while providing little or no value-added content or service to the user. These sites usually have no original content and may be cookie-cutter sites or templates with no unique content.”