Selected answers from the Dumb SEO Questions G+ community.
Jim Munro: I think the site should be making it clear to the user that the link goes to an external site. Putting external links in the menu is self-defeating. ...or at least I thought it was until other opinions were offered in this thread. :)
Loren Baker: Why would it be iffy? Lots of sites link to partner sites, their ZenDesk account or other sites in nav. My main question is, what is the purpose?
Micah Fisher-Kirshner: I wouldn`t do any nofollows for header or footer. Either have the link to the other site or not. Those links should be of value, so why would you not have it? As long as there is a good reason (sister company under a main organization for example), then it`ll be fine.