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.