not2easy - 3:53 pm on Sep 27, 2011 (gmt 0)
Your question is too broad for a simple answer. Millions of merchants and affiliates have experienced varying degrees of effectiveness. Choosing a service requires you to define your goals and research the options to find the service that best matches your goals. If your goals are undefined, all of them stand an equal chance of being right for your goals, but when you know what you want a service to do for you, you will have a basis to decide what service can help you best.
Running a self-devised tracking system will mean that affiliates may be wary of working with you if you do not have an established national brand. How can you assure affiliates that your tracking works and how do you plan to remit payments? Why should people trust you and your system? (Nothing personal!)
Overall, it appears that you could benefit by paying for the help of a consultant before spending time or money to do (or not do) something that could hurt your chances of success. There are many professional program managers and consultants able to help you formulate the basic goals and strategies for your affiliate program's success.
Like anything where consultants are not licensed, there are all kinds of consultants. Check carefully before you start, they all have a reputation if they have been in the business more than a few months.