I've got a primary site at site.com and many subdirectory "microsites" at site1.site.com, site2.site.com, etc. They are all on a single server.

Each site is to establish in the own folder under public_html and every using its own separate wordpress install.

I would like for every microsite to talk about exactly the same top level menu (the page's menu) using the primary site (I would like the microsites to any or all make use of the primary site's page menu).

I am sure you will find several approaches and Let me request you for any couple of ideas.

Being an aside, would the brand new WordPress 3. beta will make this better to do (because it combines wordpress MU in to the primary wordpress core)?

I'd most likely only use symbolic links with this.

Place your shared files in another directory (/public_html/shared) and also have the menu files for every sub-site be considered a symbolic connect to the shared menu file.