Now that a number of people are using more and more custom taxonomies for WordPress – custom taxonomy queries are something becoming necessary.
Example: You have a WordPress site set up to show/sell products (in this example – you sell books and posters). You have a custom taxonomy called “catalog” that you use to organize all the products.
If you want to show all items that are marked “posters” in your custom catalog taxonomy you can simply use this query:
query_posts( array( 'catalog' => 'posters' ) );
Of course – you can create more complicated custom taxonomy queries, but this will get you started. By using custom taxonomies (and custom post types) – you can really open the door to creating complex content management systems (and/or really cool sites that need something more than your standard categories/tags/posts/pages).
Further documentation: http://codex.wordpress.org/Function_Reference/query_posts
Remember – keep it simple!