I built a really unique and javascript intensive theme for wordpress and today shortcodes fail to work. I have no plug ins installed, therefore it is not too. What did I drop from the wordpress template files that's needed to make use of shortcodes (ie: [gallery]).

I learn how to make shortcodes, but exactly how does Wordpress take your publish and replace "[gallery]" when it's spitting it out for display?

EDIT: here's what I am presently dealing with:

    $pagepull = $wpdb->get_results("SELECT * FROM $wpdb->posts WHERE post_type = 'page' AND post_status = 'publish' ORDER BY menu_order", ARRAY_A);
    $i = 1;
    foreach ($pagepull as $single_page){
     echo "<div class=\"section\"><ul><li class=\"sub\" id=\"" . $i  . "\"><div class=\"insection\">";
         echo $single_page['post_content'];
$i++;
// more code that is irrelevant...
// more code that is irrelevant...
// more code that is irrelevant...
    }

Ok, do this

 $pagepull = $wpdb->get_results("SELECT * FROM $wpdb->posts WHERE post_type = 'page' AND post_status = 'publish' ORDER BY menu_order", ARRAY_A);
    $i = 1;
    foreach ($pagepull as $single_page){
     echo "<div class=\"section\"><ul><li class=\"sub\" id=\"" . $i  . "\"><div class=\"insection\">";
         echo apply_filters('the_content',$single_page['post_content']);
$i++;

Wordpress take your articles and apply filters into it. You have to register a filter and let parse your articles.

In case your theme isn't exhibiting your shortcodes, probabily you output this content from the publish without let Wordpress filter it.

Calling the function get_the_content() for any publish, don't run the filter for shortcodes (if any).

To possess apply

<?php apply_filters('the_content',get_the_content( $more_link_text, $stripteaser, $more_file )) ?>

Ref: http://codex.wordpress.org/Function_Reference/get_the_content

Note: many plug ins register filters using the content to implement shortcodes!