If I look at deprecated.php I see a lot of functions still being used in the core. Isn't the point of deprecating them that we shouldn't be using them anymore?
Here's a list of the functions (and between brackets the files that use them).
start_wp (wp-atom.php, wp-rss.php, wp-rss2.php, wp-admin/edit.php, wp-admin/export.php, wp-content/themes/clasdic/comment-popup.php and wp-content/themes/default/comment-popup.php)
wp_set_post_cats (wp-admin/import/dotclear.php and wp-admin/import/textpattern.php)
get_author_link (wp-includes/feed.php)
link_pages (wp-content/themes/default/attachment.php, wp-content/themes/default/page.php and wp-content/themes/default/single.php)