Remove all Div wrapper from comment form
To achieve this you need to create one template page for comment-form.tpl.php. For this you need to specify in template.php that uses template page.

&lt;?php
function phptemplate_comment_form($form) {
  return _phptemplate_callback('comment-form', array('form' =&gt; $form));
}
?&gt;


and in comment-form.tpl.php you can create your own strcution like

print drupal_render($form['name']);
print drupal_render($form['comment_body']);
print drupal_render($form['subject']);
print drupal_render($form['author']['mail']);
print drupal_render($form['author']['name']);


This works for me with register/login form.