I use a custom installation of Yoast's php script to cloak and shorten my affiliate links. The link in my page is "mysite.com/get/link1 rel=nofollow" which expands to anything from one of those huge Amazon links to a clickbank link. On my shared servers, I have one text file that does the translation for all the sites on the server, so if Share a sale drops an affiliate program, I can edit one file and change where the link goes for all the sites that may use the link.