On a lot of sites we've made all links to anything vaugely duplicated, affiliate links and anything external including anything links to other sites we own regardless of how relevant the link is to a person.
The official line is that nofollow is for links where you don't know the relevancy or quality of the external link (eg: blog comment links), but they've made things so grey that I'd recommend anything not directly related to the site not is set with this and let Google work it out.
Trev
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