Drupal 7 — Add JS with conditional comments

template.php

<?php

/**
 * Helper function to add IE commented js files.
 * Offer more placement flexibility than drupal_add_html_head.
 */
function _add_ie_js(array $scripts) {
  $return = '';

  foreach ($scripts as $key => $value) {
    $script = array(
      '#theme' => 'html_tag',
      '#tag' => 'script',
      '#attributes' => array(
        'type' => 'text/javascript',
        'src' => file_create_url($value['file']),
      ),
      '#browsers' => $value['condition'],
      '#pre_render' => array('drupal_pre_render_conditional_comments'),
    );
    $return .= drupal_render($script);
  }

  return $return;
}


/**
 * Implements hook_preprocess_html().
 */
function HOOK_preprocess_html(&$vars, $hook) {
  $ie_scripts = array();

  // Selectivizr. (For instance...)
  if ($selectivizr = libraries_get_path('selectivizr')) {
    $ie_scripts['selectivizr']['file'] = $selectivizr . '/selectivizr.js';
    $ie_scripts['selectivizr']['condition'] = array('IE' => 'lt IE 9', '!IE' => FALSE);
  }

  $vars['ie_scripts'] = _add_ie_js($ie_scripts);
}

I found this useful but it produces a self-closing tag, i.e. <script />, which doesn't work properly.

I would suggest you add '#value' => '', to your array so that you produce a separate </script> tag.