Some commentators originally suggested that affiliate links work best in the context of the information contained within the website itself. For instance, if a website contains information pertaining to publishing a website, an affiliate link leading to a merchant's internet service provider (ISP) within that website's content would be appropriate. If a website contains information pertaining to sports, an affiliate link leading to a sporting goods website may work well within the context of the articles and information about sports. The goal, in this case, is to publish quality information on the website and provide context-oriented links to related merchant's websites.
1) Gross Profit Margin – This is the first place I start. Clearly you can't offer 50% commissions on items that you only have a 20% profit margin or you'd be out of business fast (and probably in debt). So start by determining your minimum, median, and average gross profit margins on items in your store. You may also want to determine these numbers separately for each category or product type since it's possible to offer different commission rates for each product category, depending on how complex you'd like to make your program. In my experience, the simpler the better when it comes to commission structure, but technically anything's possible.