Multisite and apple touch icons
It doesn't totally help with the default paths, but I explicitly define them for each theme:

/**
 * Implements hook_preprocess_html().
 */
function MYTHEME_preprocess_html(&amp;$variables) {
  $path = drupal_get_path('theme', 'MYTHEME');

  drupal_add_html_head(array(
    '#tag' =&gt; 'link',
    '#attributes' =&gt; array(
      'href' =&gt; $path . '/images/favicon.png',
      'rel' =&gt; 'icon',
      'type' =&gt; 'image/png'
    ),
  ), 'MYTHEME-favicon');

  drupal_add_html_head(array(
    '#tag' =&gt; 'link',
    '#attributes' =&gt; array(
      'href' =&gt; $path . '/images/touch-icon-iphone.png',
      'rel' =&gt; 'apple-touch-icon',
    ),
  ), 'MYTHEME-touch-icon-iphone');

  drupal_add_html_head(array(
    '#tag' =&gt; 'link',
    '#attributes' =&gt; array(
      'href' =&gt; $path . '/images/touch-icon-ipad.png',
      'sizes' =&gt; '72x72',
      'rel' =&gt; 'apple-touch-icon',
    ),
  ), 'MYTHEME-touch-icon-ipad');

  drupal_add_html_head(array(
    '#tag' =&gt; 'link',
    '#attributes' =&gt; array(
      'href' =&gt; $path . '/images/touch-icon-iphone-retina.png',
      'sizes' =&gt; '114x114',
      'rel' =&gt; 'apple-touch-icon',
    ),
  ), 'MYTHEME-touch-icon-iphone-retina');

  drupal_add_html_head(array(
    '#tag' =&gt; 'link',
    '#attributes' =&gt; array(
      'href' =&gt; $path . '/images/touch-icon-ipad-retina.png',
      'sizes' =&gt; '144x144',
      'rel' =&gt; 'apple-touch-icon',
    ),
  ), 'MYTHEME-touch-icon-ipad-retina');
}