Thought I'd paste some of our plugin modifications here, in case you might add them to the trunk's code.
$this->path = plugins_url( '', __FILE__ );
The plugin's reliance on WP_PLUGIN_URL means that SSL throws errors.
wp_register_style( 'toc-screen', $this->path . '/screen.css', array(), '1211' ); wp_register_script( 'toc-front', $this->path . '/front.js', array('jquery'), '1211', true );
Put the script in to the footer, version stamp the version you're using whenever you update. The option to put the script at the bottom could come from the Settings page. The version number is semi-important when upgrading the plugin on servers that cache aggressively.
$html .= '<ul class="toc_list"><li><a href="#">'.get_the_title().'</a></li>' . $items . '</ul></div>' . "\n" . $items . '</ul></div>' . "\n";
This adds the title of the page to the TOC. Again, a nice option from the Settings page. This suits our heading structure well. Perhaps there's another way to include the page's <h1> on the TOC?