Welcome to WebmasterWorld Guest from 22.214.171.124
That having been said, I just did a search for "free affiliate software" and there appears to be quite a few out there. Maybe do a search for whatever software you are looking for and "review". That hopefully will give you an idea.
The trust level is super important and personally, an unknown with an in-house program and tracking doesn't exactly warm my heart.
I prefer LAMP platform i.e. php script.