Unable to print menu links using menu_navigation_links
The normal way to print that menu would be:

&lt;?php print theme('links', array('links' =&gt; $menu), 'attributes' =&gt; array('class'=&gt; array('links', 'site-menu')) ));?&gt;


or similar.

If you want to do something different for individual items then in template.php you could implement:

function THEME_preprocess_menu_link(&amp;$variables) {
    // if certain menu item, do something different
}