Are links in the body worth more than a sitewide link?
John Mueller from Google answered this question on a Google Hangout earlier this week and this is what he said.
So I think there are two aspects there, on the one hand this is the area of the page where you have your primary content, the content that this page is actually about, not the menu, the sidebar, the footer, the header... Then that is something that we do take into account and we do try to use those links. The other thing to keep in mind is you still need to make sure that within your site you have a clear linking structure. That can happen if you have a clear set up with a side bar, menu... But if you don’t have a clear linking structure, then we pick up just a bunch of links to external sites, then what might happen is we can’t really crawl the rest of your site properly because we can’t discover it properly.