one index.php for multiple application

Maybe just checking the server name would suffice. However, that won't work if you ever need to access the app via CLI, like to run a cron job, since $_SERVER won't exist. Never tried to do what you're attempting, so not sure how feasible this is.

PHP Code:

switch($_SERVER['SERVER_NAME'])
{
  case 'app1.domain.com':
    define('APP_DIR', 'application/app1');
    break;
  case 'app2.domain.com':
    define('APP_DIR', 'application/app2');
    break;
}

//Could not determine app to run, die
if ( ! defined('APP_DIR'))
{
  die('Could not determine app');
}

//If we got this far, set the $application_folder
$application_folder = APP_DIR;