Are you talking about the menus on the left? If you look at admincp/index.php, the section that starts with comment NAVIGATION FRAME, you'll see it looks for cpnav xml files in includes/xml and parses them to create the menus. Then it sorts the menus and options by display order (an attribute in the xml files). There's a hook before the sort, admin_index_navigation, where you could adjust the display orders if you want. I have no idea what interface you'd use to allow a user to arrange them.
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