Forum Moderators: skibum
There are a lot of options. You can host your own solution with affiliate scripts.
You can use built in affiliate solutions that work with your merchant services provider.
You can use a separate network like CJ.
You need to determine what types of services you need, like payment processing, specific types of stats tracking, existing affiliate base, etc. etc.
There are many options out there, and what's best for you depends on your specific needs.
I have used the shopping cart system and it worked great. I have actually never tried the affiliate software they offer but I imagine it is at a minimum satisfactory considering their other stuff is so good. Plus, most of the features are completely free.