Override favicon output
To alter or remove the favicon URL Drupal 7 points to by default (not just add another favicon link) try this:

function YOURTHEME_html_head_alter(&amp;$head_elements)
{
  // Search the head elements for the Favicon
  foreach ($head_elements as $key =&gt; $element) {
    if (!empty($element['#attributes'])) {
      if (array_key_exists('href', $element['#attributes'])) {
        if (strpos($element['#attributes']['href'], 'misc/favicon.ico') &gt; 0) 
        {
          // Change the URL
          $head_elements[$key]['#attributes']['href'] = '/'.drupal_get_path('theme', 'YOURTHEME').'/path/to/favicon.ico';

          // Or, delete the favicon link entirely
          unset($head_elements[$key]);
        }
      }
    }
  }
}