function mytheme_theme() {
    $items = array();
    $items['comment_form'] = array('comment_form' => array('arguments' => array('form' => NULL)));
    return $items;
}

<?php
  function mytheme_comment_form($form) {
    // stuff goes here
  }
?>

$form['some_markup'] = array(
  '#markup' => '<p>this is some markup</p>',
);