KowaBunga! Technologies has assembled case studies of a couple dozen affiliate programs, including Cardservice International, ClubMom, Domain Direct, and Marketing Sherpa.
The case studies cover the basic metrics of the programs, as well as questions to the respective affiliate managers about their affiliate program strategy, tracking and management decisions, goals, and experiences of the affiliate manager.
All of the affiliate program case studies are available at http://www.kowabunga.com/showcase/index.asp