I am a developer. I’m developing my own site. I’m using s2Member. I like it. I discovered, after a few days of investigation, that anything you want from an affiliate tracker you can do with a few trivial lines of PHP and Javascript.
Benefits : No fees – iDevAffiliate, which does appear to be the best choice, is $200 one time (if you can install it; it won’t install on my system) or $40 or more per month. Flexibility – No limits on what you can do with the data vs. only what the affiliate tracker product or service provider offers. Secure – Data doesn’t leave your server.
Costs : You have to do it yourself or hire someone. But this should be much less than the cost of affiliate software.
If I knew specifically what you wanted to do, I’d be happy to post the PHP and Javascript free for you, and for anyone who finds this, to do it.