How to build and organize menus with rich taxonomies and complex view-based menus
Typically, we put all of the site sections in the main menu.

Each site section will get its own Drupal menu.  How items get into menus varies widely project-to-project, but we will rely on path-alias define section organization as much as possible.

Each section will have its own Panels pages, where the site section gets used as the context / selection rule (typically by path matching), and the menu is placed in a content area.

Occasionally, we will have a site section taxonomy, which gets used inside a custom block to display the proper menu.