How to theme a menu in D7

The new theme_links($variables) function in D7 receives just an associative array to build the entire link structure, and as you can read in the documentation your "links" should be passed through the links argument as an associative array, but where and/or how do you get this array. Well, here is a example of how to do it with the user menu:

$user_menu = menu_navigation_links('user-menu'); 
print theme('links', array(
  'links' => $user_menu,
  'attributes' => array(
    'id' => 'user-menu',
    'class' => array('links', 'clearfix'),
  ),
  'heading' => array(
    'text' => t('User menu'),
    'level' => 'h2',
    'class' => array('element-invisible'),
  ),
));

If you are wondering what the 'user-menu' argument is in the menu_navigation_links($menu_name, $level = 0) function, it is the name of the menu to be printed. You can find the menu name for this example using this path /admin/structure/menu/manage/user-menu/edit on your Drupal site.

Obviously the $user_menu variable is not mandatory but doing it that way you can later use it in a conditional statement that is quite common in the templates.