Recently awarded Post Affiliate Pro is professional tool to set up and run own affiliate program. Inhouse solution that is installed on your server and provides full featured backend for you and your affiliates.

Besides being a solid affiliate software for reasonable price, it offers several advantages against other solutions:

Flash tracking - cookieless and crossbrowser tracking
Own ROI tracking - with "virtual affiliate accounts"
One-time payment for software
Support by mail, phone or online chat

It integrates easily with websites and ordering systems. 30-day money back and possibility to completely outsource set-up and integration make evey purchase risk free.