I add no follow on links to un important pages like terms and conditions and contact us pages, i figure this pushes the
PR towards the rich content. But then ill add a sitemap with standard links to all pages just so they do get indexed. Any content that you dont want indexing is easily sorted with a robot.txt file.
I dont see the point of adding no follow tags to affiliate links coz i figure any affiliates will have relevant content to you. From what i can tell google likes you to provide visitors with resources external to your own site.