List all custom post type posts from a given category?

What about doing a tax_query?

$args = array( 
       'post_type' => 'myposttype', 
       'tax_query'=> array(
            'taxonomy' => 'myposttype_categories',
            'terms' => array('foo'),
            'field' => 'slug',
        )
);
$loop = new WP_Query( $args );
var_dump($loop);

Facepalm question, you are sure that these taxonomies/post types exist and that there are posts filed under them?

Update

The query seems to work fine for me, and I am able to show a list of the posts I have added with that term/category. I moved your register_taxonomy call into the function that fires on init. Per the codex it is inadvisable to call register_taxonomy outside of an action and could be the cause of your troubles.

add_action('init', 'myposttype_register');

function myposttype_register() {

    $labels = array(
        'name' => _x('Myposttype', 'post type general name'),
        'singular_name' => _x('Myposttype item', 'myposttype item'),
        'add_new' => _x('Add Myposttype', 'myposttype item'),
        'add_new_item' => __('Add New Item'),
        'edit_item' => __('Edit Item'),
        'new_item' => __('New Item'),
        'view_item' => __('View Item'),
        'search_items' => __('Search Items'),
        'not_found' =>  __('Nothing found'),
        'not_found_in_trash' => __('Nothing found in Trash'),
        'parent_item_colon' => ''
    );

    $args = array(
        'labels' => $labels,
        'public' => true,
        'publicly_queryable' => true,
        'show_ui' => true,
        'query_var' => true,
        'menu_icon' => get_stylesheet_directory_uri() . '/article16.png',
        'rewrite' => true,
        'capability_type' => 'post',
        'hierarchical' => false,
        'menu_position' => null,
        'supports' => array('title','editor','thumbnail','page-attributes','comments','trackbacks'),
        'show_in_nav_menus' => true,
      );

    register_post_type( 'myposttype' , $args );

    register_taxonomy("myposttype_categories", array("myposttype"), array("hierarchical" => true, "label" => "Categories", "singular_label" => "Type", "rewrite" => true));

}

And the query:

$args = array(
'post_type' => 'myposttype',
'myposttype_categories'=> 'foo');

$my_query = new WP_Query( $args );

if( $my_query->have_posts() ) {
    while ($my_query->have_posts()) : $my_query->the_post(); ?>
        <p><a href="https://wordpress.stackexchange.com/questions/87111/<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a></p><?php
    endwhile;
}

wp_reset_query();

For what its worth, both of the following also work as arguments, though since you are only querying a single taxonomy you probably don’t need to use the tax_query. I used that initially because I thought you needed to find posts in both terms.

$args = array( 'myposttype_categories'=> 'foo' );

and

$args = array(
    'post_type' => 'myposttype',
    'tax_query' => array(
        array(
        'taxonomy' => 'myposttype_categories',
        'terms' => array('foo'),
        'field' => 'slug'
        )
    )
);