Disappearing Primary and Secondary Menus
I recently was performing some module upgrades on DrupalEasy.com (on a development server, of course) when I was surprised to see that both the primary and secondary links were suddenly missing.
I spent the better part of two hours going through the various modules I had updated, checking and double-checking my theme, and generally pulling my hair out.
Turns out the solution was quite simple. Somehow, the sources for both the primary and secondary links had reset to "No primary links" and "No secondary links" on Drupal's main menu settings page (admin/build/menu/settings).