Bolotomus - 10:21 pm on Sep 5, 2001 (gmt 0)
The only problem with [long duration cookies] is if you get an affiliate clickthrough with no conversion, and then the user finds you on their own later. Which is possible due to your SEO abilities.
I have clients who lose sleep over that, but I think it's a silly argument. Somebody out there is shopping around, and they come to your site through an affiliate. Later on (maybe weeks later) they are searching in Google for the very same item, they come back to your site, and they buy it. Did your affiliate serve you well? Sure they did. In fact, maybe they went to Google and looked down the list specifically for you.
I'd also like to add, one important implementation consideration is to track affiliates per invoice line, and not just per order. This is to take in account a situation where somebody fills their cart over a long period of time, and then finally makes their order. It wouldn't be fair to only pay the affiliate to happened to sell them the last item in their cart, if other affiliates were reponsible for other sales.