Q: I have a downloadable product that I want to market through affiliates. I’d like to run the affiliate software myself, instead of running through an affiliate network. What is the best software for tracking affiliate sales?
A: There isn’t a single answer there, as there are a number of variables, such as price-point, features you desire, etc.
If I was personally starting an affiliate program like you describe, I’d use either Groundbreak.com’s Ultimate Affiliate or iDevAffiliate.
Both have the essential components for running an affiliate program and are reasonably priced.
There are many other options out there, so if those don’t suit you, try querying the search engines for affiliate software and request demos from a variety of vendors.