How to alter main_menu for logged user? I would like to alter/change structure of main menu links (programmatically!) for logged in users. What is the simplest way to do this?
I hope, Drupal 7 main-menu - change item text if user logged in you check this first. 

If this does not complete your requirement, then, u have to override the theme_menu_link hook. 

http://api.drupal.org/api/drupal/includes!menu.inc/function/theme_menu_link/7

You can check whether the user is logged in or not by checking boolean $logged_in. If it is true, user is logged in else not.