Good question.
For internal links: I’d place a rel=”nofollow” tag on all internally linked pages that you don’t care are in the index. These sometimes include “About Us” pages and “Contact Us” pages. I don’t practice this, but I’ve heard of other webmasters who do it.
External Pages: I’d place a no follow on any affiliate links and other sites you don’t trust. I’d recommend doing this to affiliate links mostly.