Here are 3 affilaite solutions I found for you
http://www.affiliatetracking.com/
Remotely hosted but powerfull and cheap. First
month free so you can get setup, then $34.95 a month.
2) Ultimate Affiliate at:
http://www.groundbreak.com/
Part of their $200 a year membership (other software included too I think)
3) And a free perl script called Affiliate Master:
http://www.thewarriorgroup.com/affiliatemaster.zip