If you are looking to track sales, traffic to the different affiliate programs you are sending traffic to, i recommend you use
http://www.statsremote.com/, $29/month... huge time saver for me, you get all the programs in one window with the Stats you need.
If you are looking for your own affiliate backend (for your paysites) and want to manage affiliates that sign up to your program then
NATS is the way to go!
Hope that helps
