Change page.tpl.php in a shared theme based on domain
You could do aomething like this: 

function MYTHEME_preprocess_page(&amp;$vars)
{
    $domain = domain_get_domain();

    $vars["theme_hook_suggestions"][] = "page__" . $domain["domain_id"];
}


Feel free to explore what other values are in the $domain array and use it accordingly to make your theme suggestions as complicated as required. The above example is just to demonstrate injecting domain information.

There are developer notes on the Domain Access module as well which you may find useful