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I have Domain A (main content site, lots of content), with a domain authority of 91, and Domain B (blog of the first site, lots of content), with a domain authority of 82.  I'm merging the blog into the main domain.  Would it be best to keep it as a subdomain, or under a directory?

My site contains tens of thousands of articles, studies, multimedia files, biographies, etc.  To assist users with finding content that might be related to the page they're on, I use a side bar with 'also of interest' links to other, similar content on my site.  This is, of course, pretty standard practice. Search engines -- Google in particular -- index these pages and then include the text in the sidebar links in search results.  So, for example, on a given page I may have 20 links to related content, and the text in those links might be, 'A story about subject ABC.'  When I search for 'A story about subject ABC,' Google returns not only the page titled (and containing the content) 'A story about subject ABC.' but also every page that links to it and happens to have that link text in the sidebar. What is the proper way to handle this kind of thing?