Want to print a custom menu in Drupal 7? Berdir answer is correct. Drupal 7 theme_links function also more vastly uses arrays. For example if you would like to add another class name to the so that it is you would code it like this:
<?php print theme('links', array('links' => menu_navigation_links('menu-site-menu'),
'attributes' => array('class'=> array('links', 'site-menu')) ));?>
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