I can suggest that you join the mode S yahoo group and do a search of their site. They have a reasonably complete list.
http://groups.yahoo.com/group/Mode_S/Here is an FOI request made to the MOD which says they do not allocate the codes and directing the person to make the request to the CAA. You may wish to try the same.
http://www.whatdotheyknow.com/request/mode_s_transponder_codes#incoming-23360My advice when submitting the FOI is to request partial information instead of a request for all military codes. You would need to be clever with the types of information requested. This is because there is a limit where they will not supply any informaton if it is too big and would take more then 24 working hours to collate and research. Similarly separate requests for training fleets from requests for opertionally deployed fleets. An example would be not to ask for all Harrier codes, they are on ops and you will probably get refused on operational security grounds. However asking for all flightplans for a given day/week at RAF Cottesmore may not be refused and will contain the same kind of information.
Hope all this is helpful to you
