In my experience, Carolyn, links between subdomain and primary get the worst of both worlds.
The search engines can clearly see that two sites are interrelated so the links between them aren't entirely "natural". Therefore I don't find the links carry the full amount of their influence across (not to mention the subdomain is usually far lower authority than the primary.)
On the other hand, the search engines still seem to consider subdomains as stand-alone sites which must earn their authority on their own, so they don't directly benefit from the halo of authority of the primary site.
See what I mean by "the worst of both worlds"?
The blog post Thomas refers to is quite specifically only related to how links between subdomains and primary are reported in Google Webmaster Tools, so I'd be careful about extrapolating it too far into ranking factors. (Though in essence I agree with him that these types of links seem to function more like internal than external as far as value is concerned)
As far as the location of the links on the subdomain's page, typically links in menus & sidebars (especially if they are site-wide menus) contribute a smaller percentage of whatever influence they have than if they were a natural part of the content.
And from a user's perspective (which I prefer to think of first, before SEO considerations) it probably makes more sense to include the link to related info right in the article rather than making them go looking for it elsewhere on the page after finishing the article.
You've asked a good question, and it's answer really starts to get into the "art" part of SEO as few pure data points are viable to use when answering. Which will be why you will get a range of perspectives in the answers.
Hope that helps?
Paul
[Edited to add: If the microsite is so closely tied to the topics and purpose of the main site, it may be worth considering moving it to a subdirectory of the primary so the two sets of content can better support each other's rankings.]