You can keep the list menu sorted alphabetically by list name or you can manually re-arrange the menu and set keyboard shortcuts for individual lists by selecting the “Manage This Menu” menu item from the List menu.
To resort alphabetically click the header above the names as in any other list. You can also drag the lists manually in the list to change the order manually.
The top 9 Lists in the view will be given the keyboard shortcuts 1-9. Shortcut command-0 always opens the Master List.
The order that the Lists are shown here is the same order they will appear in all other interfaces and also in the menu on the web remotes.