One of the problem with affiliate programs such as CJ and LinkShare is the constant to need to login to the site, get the current promotions and then update the site with those snippets of html/javascript code. This is a laborious task and unless there is a good payout not worth the effort for small websites.
An alternative to this is to make use of web services such as those provided by Amazon.com to automate the content generation or use simple RSS feeds like those provided by Buy.com and create a store out of it. For example, check out this RSS feed based Buy.com Affiliate Store that generated html pages out of the Buy.com’s RSS feeds.
The choice of which route to go to pretty much depends on the type of content on your website. If you have a blog on a particular topic, hand-picking the individual products and creating affiliate links to specific links may be worth the effort. But if you are trying to be more generic, then going with a programmatic generation of your affiliate pages is much simple and effortless (except for the coding part).