I have JAM and Post Affiliate Pro on two of my sites. Both are very good affiliate scripts, but between them I like JAM a lot more. If you have no problem building your own affiliates either of those will work fine for you.

As for affiliate systems like PayGear those are hosted on their own platform. The advantage include site indexing, usually easier to get affiliates, and a broader range of services and exposer. Vendors pay their affiliates in the same manner. I have both received and paid my affiliates on the PayGear site and thus far think it’s a great service. There are other similar services out there as well as I am sure you know. ClickBank, PayDotcom, etc.