How to list custom post types in a secondary sidebar?

you can use Query Posts plugin which creates a widget that you can place on that sidebar, and select what to display.

if you are looking to code your own the its a you are sure that you wont remove it from that side bar you can create a simple custom WP_query to selset your post type and list them.
So you would need to change your code a bit like so:

<div class="block-3 border-top">
    <?php
        // A second sidebar for widgets, just because.
        if ( is_active_sidebar( 'secondary-widget-area' ) ) : ?>

            <ul id="secondary-widget" class="xoxo">
             <li><?php //your query and loop here ?> </li>

                <?php dynamic_sidebar( 'secondary-widget-area' ); ?>
            </ul>

    <?php endif; ?>

</div><!-- #sidebar -->

or you can just create your own widget and add it to the sidebar.

Hope this helps.

Ohad.