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Many merchants have nice features to their affiliate programs that act as incentives for affiliates to choose them over other similar merchants.
As an affiliate here are some things that attract me to a merchant's product(s):
1) The product's relevance to my websites
2) How high the commission percentage is and is it competitive with similar merchants?
(10% commission is better than 5%)
3) How much competition the product has (i.e.: is everybody marketing something similar?)
4) The ability to choose the landing page on the merchant's site. Because on some sites the main page is not as targeted as I'd like.
6) A product data feed
7) The ability to track the source of a lead/sale like Commission Junction does thru its SID url parameter.
8) Performance incentives. (i.e.: A bonus or higher commission for higher volume)
1) Prompt, efficient support
2) For a standalone merchant, a relatively low payment threshold - eg payment is made to the affiliate once commissions reach $25/£25 rather than having to accumulate $100/£100 or more