JROX.COM Affiliate Manager (software)
Its website may not be the most professional looking, but this affiliate manager is BRILLIANT. Best of all, it's free. You install it on your own server (uses PHP & MySQL), which makes your affiliate program look more professional to your affiliates. The knowledge base is extensive and there is a community forum for those who require assistance. The free version enables you to have up to 50 affiliates, and the premium version offers unlimited affiliates for a one-time payment of $250.