As you probably know, it is recommended to place $scripts at the bottom of the page to improve performance. Wim Leers also recommends in this patch to modify core Drupal common.inc to load jquery.js and drupal.js in the footer.
With Ubercart, I am unable to move print $scripts; to the footer of my page template, and I am unable to apply Wim's patch for the drupal_add_js function. When I try either of these, or attempt to make both of these changes, the JavaScript on the Shopping Cart pages fails.
Maybe some of this has been addressed in Ubercart 2.x, but wanted to mention it here so I can receive some feedback. Thanks.