I haven't looked into it too much since an affiliate system come built into WHMCS. There is an addon I discovered which adds more features to the existing affiliate system. I may purchase this:
WHMCS was always my go to tool. I even used it for other projects other than hosting and it helped out a lot. It helps that the feature is built in and there are add-ons to enhance it as HostShark said above me. I've tried other software and they never compared to whmcs.