<?php
function YOURTHEME_preprocess_page(&$vars) {
 
    $links = $vars['primary_links'];
 
    foreach ($links as $key => $link) {
        $links[$key]['html'] = true;
        $links[$key]['title'] = '<span>'. $link['title'] . '</span>';
    }
 
    $vars['primary_links'] = $links;
}
?>