I just dropped this into my functions.php and I now only get my custom post types showing on category requests.
function show_workshowcase( $query ) {
if ( is_category() )
$query->set( 'post_type', array( 'work_showcase' ) );
return $query;
}
add_filter( 'pre_get_posts', 'show_workshowcase' );
But, of course, standard post category requests only show the custom post type. Any ideas how I can separate the two?