If this Quicktip saves one person as much time as it should have saved me, then consider this post a success.
When setting up your Ubercart-powered site, be sure to set the input formats for the email templates correctly - otherwise the super-pretty default HTML templates that get are supposed to be sent out will instead be sent as plain, unformatted, difficult-to-read text.
You see, Ubercart ships with two default email templates - one that is used for the email sent to the admin and one that is used for the email sent to the customer when an order is placed. The customer template is nicely formatted in glorious HTML - which your customers will never see if unless you change the input setting from the default "filtered HTML" to "full HTML". For an out-of-the-box Ubercart install, you can find the input format fieldset by going to Administer|Store Administration|Conditional Actions, then click to "edit" the "E-mail customer checkout notification" action, then click the "Actions" local tab (or you can just go directly to admin/store/ca/uc_checkout_customer_notification/edit/actions).
If you want to change the text and/or format of either template, you need to open up the template file and make your changes there. You can find the template files in the ubercart/uc_orders/templates directory. Be sure to carry this file over whenever you upgrade Ubercart or you'll lose all your template changes!