You might get away with manually adding a static message to the emails by editing the content of your checkout_process.php language file.
Maybe change this, as shown:
If you want to do something more elaborate to add something to the the emails your customer receive when an order is placed, you currently need to edit a core file: /includes/classes/order.php
define('EMAIL_THANKS_FOR_SHOPPING','Thanks for shopping with us today! Also check out this offer at Susies Shoes website: www.her_site.com ');
At the end of the file is the code which assembles and sends the emails.
You'll have to roll up your sleeves and do some custom programming.