So this one is rather old in 2013. But then again Ubercart and E-commerce are slowly getting up to speed with drupal 7 so still many sites use Drupal 6 for web shops. Anyhow, what we wanted to do is add some extra information to emails sent after order. Ubercart has a way of sending nice HTML emails to clients and obscure plain text emails to admins. Which is ok by me and in drupal 7 it is easily replaced and set up by additional email modules like MailSystem I think https://drupal.org/project/mailsystem which integrates with UberCart in drupal 7. There is Mailsystem for drupal 6 also, but not sure if this works. Anyway for both drupal 6 and 7 email templates are in ubercart/uc_order/templates
so this is where you should head. Open all of them. One is empty. One is for clients and one is for admin uc_order-admin.tpl.php So to quickly add some variables there, check the other one that is for clients, well customers uc_order-customer.tpl.php and pick variables frome there and add it to uc_order-admin.tpl.php template. My client wanted to have shipping address in order email, so he doesn't have to log in drupal system just to check it and invoice he got from paypal sometimes isn't correct and shipping address was not the same as the one in order.