In Toad 11.6 when you are in the File | Open file window, you can right click and select Sort by | Descending and it will list the files first and keep this setting. In Toad 12 the option to Sort by has been removed so you can't sort for the file on top.
WORKAROUND:
None.
STATUS:
Waiting for a fix in a future release of Toad for Oracle.