Drupal 6: Move the 'Add new comment' link to the bottom
Since Drupal is such a highly configurable system, there are a few ways to accomplish what you want. Here's just one example.

The first part of the equation is to remove the link from the node's links array. This approach removes it during the theme call.

&lt;?php
/**
 * Override theme_links() so we can remove or alter any links we don't need.
 */
function MYTHEME_links($links, $attributes = array('class' =&gt; 'links')) {
  unset($links['comment_add']);

  // Rather than include all the original theme_links() code in this function,
  // we can just call it directly here.
  return theme_links($links, $attributes);
}
?&gt;


After that, you have a few options of where to readd the link. The primary function that builds the display for comments and comment controls is comment_render() in comment.module. It builds the comments display using a few different theme calls, so it's up to you where you want to add the link back in. Probably the easiest approach is to copy the file /modules/comment/comment-wrapper.tpl.php into your theme folder and add the code for the link there. Alternatively, you could either put it above or below the comment controls form (by overriding theme_comment_controls), or by overriding any of the other comment theme functions. Whichever approach you take to adding the link back in, you can get the code for the link from the comment_link() function -- open up comment.module and search for "Add new comment" to find the link code.

Good luck!