Control content before and after custom post type loop

When you initiate a Loop, split it up like so:

<?php if (have_posts()) : ?>
           <?php while (have_posts()) : the_post(); ?>    
           <!-- do stuff ... -->
           <?php endwhile; ?>
 <?php endif; ?>

Anything inside the if statement but outside the while statement will run if have_posts is true, but will not be Looped for each Post.

Also, it’s recommended that you use WP_Query, not query_posts – see here for more information. Be sure to reset the Loop after your query – it’s recommended here that wp_reset_postdata is the best option when using WP_Query.

So, in conclusion you should be writing something like this:

<?php

// Your arguments    
$args = array(
    'post_type' => 'stuff',
    'taxonomy' => 'stuff-type',
    'term' => 'new-stuff',
    'orderby' => 'date',
    'order' => 'DESC',
    'posts_per_page' =>-1
);

// Let's get the query, using WP_Query
$loop = new WP_Query($args);

// Check if there are posts for our query
if ( $loop->have_posts() ) : ?> 

<h2>New Stuff</h2>
<ul>

    <?php 
    // Get looping    
    while ( $loop->have_posts() ) : $loop->the_post(); ?>

    <li><a href="https://wordpress.stackexchange.com/questions/99859/<?php the_permalink(); ?>"><?php the_title(); ?></a></li>

    <?php endwhile; ?>

</ul>     

<?php endif; ?>
<?php wp_reset_postdata(); ?>

Hope that helps!