I actually wrote a small php script that powers the affiliate program I use at
phpArcadeScript. Nothing too fancy about it, but it does track sales generated from affiliate links. It will improve as the company grows, but its a very easy solution for the time being.
I have looked into the ClickBank type programs, and they are also very good solutions and could open the doors for sales a lot easier than doing it yourself ... but you lose some control over your program if you have someone else do it.
So that's really the trade-off ... control vs. # of affiliates... right now, like the support I give to my projects, I want my customers to know that I am always available to provide the support and its coming from someone who actually knows the product ... make sense?
Scott