The best affiliate website could be designed keeping in mind that it is going to have some banner ads, pop-up ads, affiliate links, or a header ad depending upon the choice of an affiliate user. The thing that should need to be careful is design should look simple and there are space for the banner, headers, links or whatever the method you chose to sell the affiliate product won't give a clumsy look to the entire website.
I have seen many sites with loads of flashing banners, people don't stand with those sites, everyone need peace and simple website to read.
