I fixed ul nesting

I didn’t want to bother figuring out SVN and Trac, so here’s a new version of the plugin that fixes ul nesting.

<?php
/*
Plugin Name: BE Subpages Widget
Plugin URI: http://www.billerickson.net
Description: Lists subpages of the current section
Version: 1.2.2
Author: Bill Erickson
Author URI: http://www.billerickson.net
License: GPLv2

2013-09-24 - Minor edits by Jordan Bradford to fix <ul> nesting; resolves http://wordpress.org/support/topic/active-sub-sub-page-link-has-empty-under?replies=1
*/

/**
 * Register Widget
 *
 */
function be_subpages_load_widgets() {
	register_widget( 'BE_Subpages_Widget' );
}
add_action( 'widgets_init', 'be_subpages_load_widgets' );

/**
 * Subpages Widget Class
 *
 * @author       Bill Erickson <bill@billerickson.net>
 * @copyright    Copyright (c) 2011, Bill Erickson
 * @license      http://opensource.org/licenses/gpl-2.0.php GNU Public License
 */
class BE_Subpages_Widget extends WP_Widget {

    /**
     * Constructor
     *
     * @return void
     **/
	function BE_Subpages_Widget() {
		load_plugin_textdomain( 'be-subpages', false, basename( dirname( __FILE__ ) ) . '/languages' );
		$widget_ops = array( 'classname' => 'widget_subpages', 'description' => __( 'Lists current section subpages', 'be-subpages' ) );
		$this->WP_Widget( 'subpages-widget', __( 'Subpages Widget', 'be-subpages' ), $widget_ops );
	}

    /**
     * Outputs the HTML for this widget.
     *
     * @param array, An array of standard parameters for widgets in this theme
     * @param array, An array of settings for this widget instance
     * @return void Echoes it's output
     **/
	function widget( $args, $instance ) {
		extract( $args, EXTR_SKIP );

		// Only run on pages
		if ( !is_page() )
			return;

		// Find top level parent and create path to it
		global $post;
		$parents = array_reverse( get_ancestors( $post->ID, 'page' ) );
		$parents[] = $post->ID;

		// Build a menu listing top level parent's children
		$args = array(
			'child_of' => $parents[0],
			'parent' => $parents[0],
			'sort_column' => 'menu_order'
		);
		$depth = 1;
		$subpages = get_pages( apply_filters( 'be_subpages_widget_args', $args, $depth ) );

		// If there are pages, display the widget
		if ( empty( $subpages ) )
			return;

		echo $before_widget;

		global $be_subpages_is_first;
		$be_subpages_is_first = true;

		// Build title
		$title = esc_attr( $instance['title'] );
		if( 1 == $instance['title_from_parent'] ) {
			$title = get_the_title( $parents[0] );
			if( 1 == $instance['title_link'] )
				$title = '<a href="' . get_permalink( $parents[0] ) . '">' . apply_filters( 'be_subpages_widget_title', $title ) . '</a>';
		}	

		if( !empty( $title ) )
			echo $before_title . $title . $after_title;

		if( !isset( $instance['deep_subpages'] ) )
			$instance['deep_subpages'] = 0;

		// Print the tree
		echo '<ul>';
        $this->build_subpages( $subpages, $parents, $instance['deep_subpages'], $depth );
        echo '</ul>';

		echo $after_widget;
	}

	/**
	 * Build the Subpages
	 *
	 * @param array $subpages, array of post objects
	 * @param array $parents, array of parent IDs
	 * @param bool $deep_subpages, whether to include current page's subpages
	 * @return string $output
	 */
	function build_subpages( $subpages, $parents, $deep_subpages = 0, $depth = 1 ) {
		global $post, $be_subpages_is_first;
		// Build the page listing
		//echo '<ul>';
		foreach ( $subpages as $subpage ) {
			$class = array();

			// Set special class for current page
			if ( $subpage->ID == $post->ID )
				$class[] = 'widget_subpages_current_page';

			// First menu item
			if( $be_subpages_is_first )
				$class[] .= 'first-menu-item';
			$be_subpages_is_first = false;

			$class = apply_filters( 'be_subpages_widget_class', $class, $subpage );
			$class = !empty( $class ) ? ' class="' . implode( ' ', $class ) . '"' : '';

			echo '<li' . $class . '><a href="' . get_page_link( $subpage->ID ) . '">' . apply_filters( 'be_subpages_page_title', $subpage->post_title ) . '</a>';
			// Check if the subpage is in parent tree to go deeper
			if ( $deep_subpages && in_array( $subpage->ID, $parents ) ) {
				$args = array(
					'child_of' => $subpage->ID,
					'parent' => $subpage->ID,
					'sort_column' => 'menu_order'
				);
				$deeper_pages = get_pages( apply_filters( 'be_subpages_widget_args', $args, $depth ) );
				$depth++;
                if($deeper_pages != null) { echo '<ul>'; }
				$this->build_subpages( $deeper_pages, $parents, $deep_subpages, $depth );
                if($deeper_pages != null) { echo '</ul>'; }
			}
            echo '</li>';
		}
		//echo '</ul>';
	}

	/**
	 * Sanitizes form inputs on save
	 *
	 * @param array $new_instance
	 * @param array $old_instance
	 * @return array $new_instance
	 */
	function update( $new_instance, $old_instance ) {
		$instance = $old_instance;

		/* Strip tags (if needed) and update the widget settings. */
		$instance['title'] = esc_attr( $new_instance['title'] );
		$instance['title_from_parent'] = (int) $new_instance['title_from_parent'];
		$instance['title_link'] = (int) $new_instance['title_link'];
		$instance['deep_subpages'] = (int) $new_instance['deep_subpages'];

		return $instance;
	}

	/**
	 * Build the widget's form
	 *
	 * @param array $instance, An array of settings for this widget instance
	 * @return null
	 */
	function form( $instance ) {

		/* Set up some default widget settings. */
		$defaults = array( 'title' => '', 'title_from_parent' => 0, 'title_link' => 0, 'deep_subpages' => 0 );
		$instance = wp_parse_args( (array) $instance, $defaults ); ?>

		<p>
		<label for="<?php echo $this->get_field_id( 'title' ); ?>"><?php _e( 'Title:', 'be-subpages' );?></label>
		<input id="<?php echo $this->get_field_id( 'title' ); ?>" name="<?php echo $this->get_field_name( 'title' ); ?>" value="<?php echo $instance['title']; ?>" />
		</p>

		<p>
			<input class="checkbox" type="checkbox" value="1" <?php checked( $instance['title_from_parent'], 1 ); ?> id="<?php echo $this->get_field_id( 'title_from_parent' ); ?>" name="<?php echo $this->get_field_name( 'title_from_parent' ); ?>" />
			<label for="<?php echo $this->get_field_id( 'title_from_parent' ); ?>"><?php _e( 'Use top level page as section title.', 'be-subpages' );?></label>
		</p>		

		<p>
			<input class="checkbox" type="checkbox" value="1" <?php checked( $instance['title_link'], 1 ); ?> id="<?php echo $this->get_field_id( 'title_link' ); ?>" name="<?php echo $this->get_field_name( 'title_link' ); ?>" />
			<label for="<?php echo $this->get_field_id( 'title_link' ); ?>"><?php _e( 'Make title a link', 'be-subpages' ); echo '<br /><em>('; _e( 'only if "use top level page" is checked', 'be-subpages' ); echo ')</em></label>';?>
		</p>

		<p>
			<input class="checkbox" type="checkbox" value="1" <?php checked( $instance['deep_subpages'], 1 ); ?> id="<?php echo $this->get_field_id( 'deep_subpages' ); ?>" name="<?php echo $this->get_field_name( 'deep_subpages' ); ?>" />
			<label for="<?php echo $this->get_field_id( 'deep_subpages' ); ?>"><?php _e( 'Include the current page\'s subpages', 'be-subpages' ); ?></label>
		</p>

		<?php
	}	

}

http://wordpress.org/plugins/be-subpages-widget/