Few years ago I saw a big article about all affilate programs at shops. Author even made a experiment with his high traffic site. He put a banner for amazon shop, and he got only some 30 dollars from that day, while his site earned hundreds per day with normal advertising. For us, with small sites there is no alternative as no one will pay as per impresion. Maybe sometimes we get to pay by click... Just to give you an idea on how profitable is/or not/ amazon affilate program is.
Amazon is definitely a good program, but you really have to work at it. The Amazon API is the best way to place affilite links on your site, because you don't have all the amazon banners and you can effectively place ads on your page to get a better response from visitors.
For an example page setup using a perl script that queries Amazon API and how seamlesly Amazon content can be flowed into a site check out the Code4Gold Books Section...
Looking forward to seeing more on this... I have been using simpler methods of posting links, or associating links with images. A website generator that would incorporate the Amazon content within the site itself would be a great asset!