We are not lawyers nor based in the EU, but from what we understand, this new regulation exempts cookies which are necessary to provide a service that the site user has deliberately requested, such as setting a cookie to keep track of a buyer's order details in providing a shopping cart service to them. This cookie is set by the seller's page (via our box.js cart script) for the seller's domain if they are using our standard overlay-style cart.
In the case of affiliate cookies, it's actually our US-based server that sets the referral cookie after clicking the affiliate link, and before we redirect the user to the seller's landing page, so sellers subject to this EU cookie directive should be unaffected in that case as well.
I found some analysis and tips here that you may find of interest:
http://www.compactlaw.co.uk/free-legal-articles/eu-cookie-law-regulations.html