General Guidelines for Threat Identification

Is it a friendly? Or is it an enemy?
This is probably the single most important question dealing with the identification of threats. The best way to avoid fratricide incidents is to be aware of the location of friendly and enemy units on the battlefield. For instance, if your mission brief and map show that no friendly units are on the attack and they are all positioned on the friendly side of the FEBA, then as a general rule, anything beyond "the fence" will be an enemy target. There are occasions where friendly units will stray across the FEBA, but they will almost definitely stay within 1km of friendly lines unless they are on the attack. Also, as a general rule of thumb, vehicles on the front lines will almost always face towards the FEBA. Although there are a few exceptions to this in the game, for the most part, if it's facing your side of the FEBA, it's a threat vehicle.
The difficulty of threat identification on CAS missions
The most difficult, and most important, time to differentiate between friend and enemy is when you are supporting attacking or defending ground units. In both of these instances, you will have both friendly and enemy units on the same side of the FEBA. The simplest way to maintain positive control is to stay close to, or just in front of, friendly units, so that anything ahead will be an enemy. During offensive CAS, it is usually a good idea to stay ahead of your own units, thereby giving yourself time to deal with threats, as well as being able to be relatively sure that anything in front of you is an enemy. Another key is to note the direction of movement of the units. On an offensive CAS, enemy units will usually be stationary in the defense, with friendly units traveling at a fairly high speed. The opposite is true in the case of a defensive CAS, where friendly units will normally remain stationary in defensive positions, as the enemy units keep moving. In both cases, however, once friendly an enemy units begin mingling in close proximity, it becomes very important to use your TADS for positive identification of targets.
Are those our helicopters?
If you have to ask yourself this question, then you should have paid more attention to the pre-mission briefing and map. You should be acutely aware of where your other friendly aircraft will be flying at all times, especially if their flight paths are near yours. By the time you will be able to visually identify an aircraft as friend or foe, it will already be engaging you, so it is paramount that you keep yourself aware of the locations of your other flights. Although I consider this a slight cheat, using the in-flight mission map will give you the current locations of all your flights, but it can easily justified by the fact that you are unable to call the other flights for a location report.