From http://wordpress.stackexchange.com/questions/20580/disable-update-notification-for-individual-plugins

new_gist_file.php

//remove update notice for forked plugins
function remove_update_notifications($value) {
    if ( isset( $value ) && is_object( $value ) ) {
        unset($value->response[ plugin_basename(__FILE__) ]);
    }

    return $value;
}
add_filter('site_transient_update_plugins', 'remove_update_notifications');