I don't really know of any stand alone affiliate programs. I just finished integrating WHCMS into my site which has a built in affiliate program. This was the easiest integration that I have ever done.
However, I have not used the affiliate program yet in WHCMS. All of the other features are top notch and I would expect the affiliate program to be the same.
I would definitely recommend JAM (Jrox Affiliate Manager)
This is free (still full-feature) for 50 affiliates, then you will need to buy the license.
But they will give some generous discount on some occasions such as "ThanksGiving Day", or "New Year" etc. so don't hurry to buy the license and subscrbe for their newsletters to be notified for special discount.
You can integrate JAM with lots of billings softwares or shopping carts listed in their manual.
PS. sorry I could not give you the link to JAM website because I have less than 5 posts which is a stupid rule! run a search in google and you will find it.