If you are talking about managing your own Affiliate program, JROX Affiliate Manager (JAM) Software is probably one of the best out there. They have a free version that is limited to... 500 affiliates (I think..) and cost 200US to upgrade (and if you need to go beyond the 500, I would imagine you can afford it at that point) With JAM you can do pretty much everything under the sun that you need to do, and it ties into most payment processors with ease. The documentation is a little scarce, and the support people on the forums are a little brash, but they answer a question directly and as helpfully as possible. jam.jrox.com or Google JROX Afililiate Manager Now if you are talking about managing aff programs you belong to? Sorry, can't help you there
postaffiliate.com also have free version. Full version is 99$ - running on php. aspxsoftware.com - running on asp, starting at 85$ softservice.org - running on php - just 49$
The bad thing with using free affiliate software is that you may find it much harder to get affiliates and especially the bigger ones. This is because if you can't afford to buy the affiliate tracking software then they will think how will you end up affording to pay your affiliates. Good luck anyway.