One of the common pet peeves over in wp.com land is how if you have a static front page, the page that you use gets listed twice in wp_list_pages if the theme uses a static home link like most of them do.
Here's a work around:
<?php
$tmpexclude = get_option('page_on_front');
$tmpline = 'sort_column=menu_order&depth=1&title_li=&exclude=' . $tmpexclude;
wp_list_pages($tmpline);
?>
Gotta admit that you have to do this in each theme while adjusting the content of the $tmpline.
Anyone care to tackle this in core code?