I was documenting the changes today and creating a new demo module to replace the old favorite band module when I realized there was no way to easily create settings forms for checkout panes. I mimicked the payment method system and added in a 'settings' $op to the checkout pane callbacks. Now, you can return an array of form element arrays with that $op and these will be added to the bottom of the checkout panes form at admin/store/settings/checkout/edit/panes. The demo module has been posted here:

http://www.ubercart.org/contrib/670