Old: <div class=”post”>
New: <div <?php post_class() ?>>
Found: multiple files
Display the classes for the post div e.g class=”sticky category-uncategorized tag-untagged”. Using this function will break your theme on older version of Wordpress (< v2.7). Not using this, however, you are unable to style your individual sticky/category/tag post. Workaround would be to do a if function_exists() check.

Old: <?php include (TEMPLATEPATH . ‘/searchform.php’); ?>
New: <?php get_search_form(); ?>
Found: multiple files
Will first attempt to locate the searchform.php file in either the child or the parent, then load it. If it doesn’t exist, then the default search form will be displayed. Probably can safely ignore this for now because if you use this template function, your theme will not be backward compatible to older version of Wordpress (< v2.7).

New: <link rel=”alternate” type=”application/atom+xml” title=”<?php bloginfo(‘name’); ?> Atom Feed” href=”<?php bloginfo(‘atom_url’); ?>” />
Found: header.php
Add Atom feed link

New: <?php if ( is_singular() ) wp_enqueue_script( ‘comment-reply’ ); ?>
Found: header.php
Add script for threaded comments if current page is a single post, is a page, or is an attachment.

New CSS classes in style.css, mainly for the threaded comments
.thread-alt {
.thread-even {
.depth-1 {
.even, .alt {
.commentlist li ul li
#commentform {
#respond:after
.commentlist li ul li
.children

comments.php: Major code changes. I think this post on Wordpress 2.7 Comments Enhancements will do a better job of explaining the changes.