Your choice for cost will be dependent upon the volume you expect and the amount you are paying. If success in affiliate programming is a numbers game, then Link Share is the leader with more than 200,000 affiliates. Also note that if you divide the number of merchants who are competing for affiliates with the number of affiliates, the resulting ratio is even more favorable for Link Share. In April 200 we did a comparison between bCentral and Commission Junction. One of them attained a 30 times greater sign-up rate.
Customer service is a major factor in choosing to partner with any affiliate program.
One of these companies has the worst service of any company, bar none. You won't find any phone numbers to call because they don't want you to bother them. Send them an e-mail and you may as well go on vacation. Another company is very service oriented. They give you e-mails, phone numbers, a personal rep, and send you presents from time to time.