You can easily code in a metatag to display on certain domain only when use domain access module. Valid example for this is when you have a multiple domain installed on the same directory and utilizing domain modules to switch between different domain, and you don't want Google or any search engine robot to crawl some domain.

You may argue that this can be done via robot.txt, and for multiple domain some fancy .htaccess rule with redirection to different robot.txt files for each of the domains respectively. The answer is yes, you can achieve the same results with this way too.

Anyway, to code in different metatags to use in different domain under domain access :

// This function will check for current domain and give
// custom html markup to Drupal head

  if (module_exists('domain')) {
    $allowed_domain = array(
    	'somedomain.com',
    	'anotherdomain.com',
    );

    $active_domain = domain_get_domain();

    if (!in_array($active_domain['subdomain'], $allowed_domain)) {
      // You can change the metatags markup here
      $robot_noindex = array(
        '#type' => 'markup',
        '#markup' => '<meta name="robots" content="noindex" />' . "\n",
      	'#weight' => 12,
      );

      drupal_add_html_head($robot_noindex, 'noindex');
    }
  }

You can put the function in template_prepocess_html or hook_init() in your theme template.php (assuming you are using one theme for all domains) or in a custom modules.