How can i retrieve all custom registered taxonomy?

The built-in taxonomies are registered with the parameter _builtin set to TRUE. To get all custom taxonomies, ask for '_builtin' => FALSE:

add_action( 'wp_footer', function()
{    
    $taxonomies = get_taxonomies( array( '_builtin' => FALSE ) );
    print '<pre>' . print_r( $taxonomies, 1 ) . '</pre>';
});