I've done a fair bit of searching for a good open-source affiliate system, and the short answer is no, there aren't any yet that are really good.
There are, however, some decent efforts out there, so you might have a look at them instead of starting completely from scratch.
http://sonicfog.com/sonic_affiliate.php
http://www.web-bureau.com/modules/fr...ing-script.php
http://www.webradev.com/postaffiliate/
For comparison, the best commercial system I've found is
AssocTrac from Internet Marketing Center.
If you do get a quality open-source affiliate system going, I'd love to hear about it!