Back in the -10, each squadron had a list of callsigns assigned to that unit. Each flight leader "bought" his own callsign at a callsign auction (these are flight callsigns, not personal callsigns), that the squadron held every so often. So you could tell who was who based on their flight callsign on ATC freq. My original assigned was "Airwar", so each time I flew, my flight would be Airwar 1/2, or 1/2/3/4. In my new plane, we'll fly with "Ghost", "Nightmare", etc. Operationally, within a combat theatre, each squadron will be assigned their own callsign that all their planes will use, so that squadron can be identified by others....the different flights are noted by different numbers; ie- Monkeyspanker 31 flight, being different from Monkeyspanker 51 flight.
The USN and USMC do it the same way the USAF does it in combat. Each squadron has it's own callsign, and the squadron planes use that callsign along with the nose number of the particilar aircraft, ie- F-5s from VMFT-401 at Yuma MCAS use the callsign "Sniper", whereas the AV-8 Harriers from VMA-211 use the callsign "Wake". So Harrier number 05 from 211, Wake 05 flight, with #2 being "dash-2".