I am not a Joomla/CB/open source master by any means, but I have put together a handful of great websites using these tools. From what I've seen, the free parts are free for the community to use, but it seems like good form to pay for the components that will be getting YOU paid. For example, I had no problems paying for CBSubs, since I am using it to generate revenue. I am also going to be installing an affiliate program and I will expect to pay for it... simply because it will be generating income for me.
With that in mind, I will be either using iDevaffiliate or PostAffiliatePro4 which are the two that the CB developers have recommended. I believe that the headaches I will avoid using a tested affiliate program will be worth the cost.