You should use 2 queries for this:

    $excluded = query_posts( array(
            'meta_key=> 'clpr_excoupon';
            'meta_value' => '0'
    ) );

    $paged = (get_query_var('paged')) ? get_query_var('paged') : 1;
    query_posts( array(
        'post__not_in => $excluded;
        'post_type' => APP_POST_TYPE,
        'post_status' => 'publish',
        APP_TAX_STORE => $term->slug,
        'ignore_sticky_posts' => 1,
        'posts_per_page' => -1,
        'paged' => $paged
    ) );

with this code you will get all the posts that have the clpr_excoupon with value 1 :)

Hope this helps...

Cheers,
Mile