Nofollowing your links to cut off different sections of your site is something that doesn’t matter unless you have a lot of link juice to throw around in the first place. If amazon.com nofollowed? It’d be unstoppable. Now if joeblowscomputerwarehouse.com nofollowed, it’d barely have an impact.

Internal structure first and foremost should deal with keyword and anchor text. Deal with nofollowing later.

So if you’re pretty sure you can handle it (sometimes you can cut off main parts of your site and cause search engines to “miss” some good links), here’s how I look at it:

What pages are not going to be ranking for jack, and have no need to distribute PR? Those are your nofollows. About me, contact us, privacy policy. Optionally categories and whatnot. If you’re trying to rank the homepage, concentrate on eliminating as many dofollow internal links (within reason) to the longtail pages. Trying to rank for longtail? Do the same but with articles. Nofollow out categories and whatnot.

Trying to mix it? Just get rid of the nasty pages.