how to send multiple attachments with drupal_mail_system I can programmatically send emails with an attachment with problem.  But after searching I can not seem to find the solution of how to attach multiple files. Does any one have the code to this.  

Here's the working code I have for sending email.

$mail = variable_get('site_mail', '');  // sets the site wide email address

      $my_module = 'Email Application';
      $my_mail_token = microtime();
      $from = $sender;  
      $message = array(
        'id' =&gt; $my_module,
        'to' =&gt; $app_email,  
        'subject' =&gt; $subject,
        'body' =&gt; $body,
        'headers' =&gt; array(
          'From' =&gt; $from, 
          'Sender' =&gt; $from, 
          'Return-Path' =&gt; $from,
  ),
  );

$message['attachments'][] = drupal_realpath($attachment_path);

$system = drupal_mail_system($my_module, $my_mail_token);
You're using $messages['attachments'] as an array, so presumably just add another item to the array:

$message['attachments'][] = drupal_realpath($attachment_path);
$message['attachments'][] = drupal_realpath($another_path);
$message['attachments'][] = drupal_realpath($yet_another_path);