The Main menu should be used to separate the content on the site into easily navigable categories. This helps users find what they are looking for quickly and painlessly.

Typically the main menu is used to divide up the main branches of an organization.  For example, an academic organization might have a main menu layout that looks something like:

Home    About    Programs/Schools    Research    Directory   Events   Contact Us

Whereas an administrative unit might have a main menu that looks something like:

Home    About     Services   Directory   Events    Contact Us

The Main menu can then have drop-down items that further sub-divide the main items.