You can activate the menu sort Function in the table SSM_CUST with the switch "SORT_USER_MENU". This activates the sort for all users in the system. However the function requires redundancy check to be activated (snote 322853).
You can activate several addional switches concerning the menu:
ALL_USER_MENUS_OFF
SAP_MENU_OFF
CONDENSE_MENU (if you have duplicated folders this migth be an option to consider, snotes 203994, 357693)
SORT_USER_MENU (see above, snotes 322853, 334993)
DELETE_DOUBLE_CODES (if you want to get rid of double tcodes, snotes 357877, 1246860)
The actual settings require more information on your authorization and user experience model. However they should be done in a project changes to these settings affect all users and should include key users as well as sap security consultants. They could really have an implication on the process as it could changes the way users are working in the system and so... I assume you know what I am talking about.
PS: I am not aware of other options to do this other than in alphabetical order.