They're also shown by relevancy - e.g. if you search for "terranetwork" they are shown on our entry, but if you search for "zencart hosting" they are not.
If you sign up to the Google Developer Tools (sitemap) stuff, then you'll see what links exist for your site. You can't modify them (only delete) though. The Google Webmaster Tools are here:
Google Webmaster Central
From experience, it looks like Google usually takes the top-level navigation as basis e.g. a header which is included on all pages.