I don't have any formal testing to back these observations. These are simply what I have noticed by experimenting with affiliate programs for twenty years.
** I believe that google strongly dislikes "thin affiliate" websites. These are sites that are monetized by affiliate links but that have very little real content or low value content. I believe that they are subjected to a "quality filter" that is more strict than the "Panda" algorithm.
** If you link to affiliate websites, expect those links to drive the affiliate site higher in the organic SERPs. So, if you are competing in the organic against the affiliate program site, you will empower them at your own expense.
** I have used Adsense on all of my websites since the first week that Adsense was available. I've learned how much money different ad positions on the page can produce with Adsense, then I have compared that to what affiliate ads produce in the same position. Adsense almost always make more money - not a little more money, a lot more money.
** I have also compared the amount of money that I can make using affiliate links to the amount of money that I can make by stocking the product and filling the orders myself. I make a lot more money filling the orders myself. There is no comparison.
** What I have not tested is how much can be earned by using hypertext affiliate links within the paragraphs of my content. In those locations, I am using links to sales pages on my own website or to articles on my site that are relevant to the links. I am confident that the sales links to products that I sell and fulfill myself will make a lot more money. I think that links to my own article content are valuable, but if they are more valuable than a small commission, I can't answer - but I'd rather keep the visitor on my own website.