Michael, start here:
Grab the download at the top of the list, FS9 text files.
That will give you the complete listings of the STOCK FS9 variants for the ATC.
If your install of FS is in a different language, your mileage
may vary but I think you'll be OK.
The rest of this comes down to what you would
expect ATC to say.
Let me start out with a modern ATC environment.
Suppose we're talking about an F-16.
The aircraft.cfg file would look like this:
[fltsim.42]
title=VIPER 120fw
sim=F-2
model=fuel
panel=
sound=
texture=120fw
checklists=
description=F-16 Fighting Falcon ---by Kirk Olsson---\n120fw repaint by Paul Schwerdtfeger
ui_manufacturer=Lockheed Martin
ui_type=F-16C viper (USAF)
ui_variation=120fw MTANG KGFA
atc_heavy=0
atc_id=1
atc_airline=PISTOL
atc_flight_number=278
atc_parking_types=MIL_COMBAT
atc_parking_codes=120FS
[General]
atc_type=LOCKHEED
atc_model=F16
You, ATC, the Tower, and Ground would say
"Pistol two seven eight, Lockheed Eff sixteen".
For WWII and earlier military planes, this gets a little more tricky. But, we can cheat the system a little.

The "atc_flight_number" line gives you some more latitude when it comes to ATC. While the airline, type, and model lines are "locked" to the available entries in the FS voice file, you can use numbers
and letters in the flight_number line in whatever combination you want.
As an example, let's look at an allied P-47 Thunderbolt from WWII.
Suppose the ID code on the fuse is "E2-N".
My convention for the older warbirds is that the tower and ground would call you
what they can see.
In this case, the .cfg would would look like:
[fltsim.5]
title=P-47D-30-RE #71
sim=P-47D-30
model=30
panel=
sound=
texture=#71
kb_checklists=P-47D-30_check
kb_reference=P-47D-30_ref
atc_id=227266
ui_manufacturer=Wings of Power
ui_type=P-47D
ui_variation=324th FG/ 316th FS #71
description=Wings of Power Republic P-47-D-27-RE #71 #42-27266, 316th FS, 324th FG, 12th AF, France 1945.
atc_heavy=0
atc_airline=
atc_flight_number=E2N
atc_id_color=0x00000000
atc_parking_types=MIL_COMBAT
atc_id_font=Verdana,-11,1,600,0
visual_damage=0
prop_anim_ratio=2.43174
[General]
atc_type=REPUBLIC
atc_model=P47
Note that "airline" line is blank. ATC would call this plane "Echo two November" and "Republic P forty seven".
Another variation might be handy for Axis and Post-war Warsaw Pact aircraft with colored "buzz" numbers on the fuse.
You would need some edited Airline voice files for colors like red, black, white, green, blue, and yellow.
You would also need the "buzz" number in the flight number line. This would let ATC call the plane "Blue four nine".