Many ships have a squadron of one of these, activated by pressing '3'.

If you haven't yet selected a target, upon launch they will be set to defend your ship, flying in formation around it, looking pretty cool.

You can also send them to defend your team mate's ships, attack enemy ships, or to engage enemy fighters/bombers/drones, depending on their function.

Select a target by pressing 'T', then send your squadron to it by pressing '3'.

Pressing 'R' once will call them back to defend your ship, or they will do this automatically once their target is destroyed, gone from the map, or cloaked.

Pressing 'R' a second time will retrieve them back into your ship, where they will be repaired.
THIS IS IMPORTANT BECAUSE: if your squadron is destroyed, their cooldown timer will be longer than if you had manually retrieved and repaired them.

In the next few sections I will explain how each type of squadron can be used, what you'll want to target with them, and when you might want to retrieve them.

All fighter squadrons are essentially the same. Small attack ships that deal tiny amounts of damage. Some question just what the hell they're good for...

They can be used in 3 ways.

1. to defend your ship from other enemy fighters, bombers & drones.
With your fighters in formation by your side, they will automatically engage other enemy squadrons that target your ship. If you combine this with your point defense system (PDS), it will make quick work of the enemy squad, whittling them down in seconds.
Your fighters can also do the same for an ally. Just target them and activate the fighters.

2. to directly engage other enemy squadrons.
This is perhaps their most valuable, effective use. If you see drones buffing or assisting enemy ships (such as healing or tugboat drones), or harassing your allies (such as bombers, slow drones or syphon drones), target the enemy squadron, and send out your fighters. They'll usually finish them off faster than a PDS.

3. to harass an enemy ship.
This is useful for 3 reasons. Firstly, to allow your missiles to hit their target. The enemy PDS can only target so many fighters or missiles at once. This is particularly useful if you want to land the Brawler's harpoon, for example.
Secondly, to drain their energy. Using PDS against a squadron consumes significant amounts of energy. This can be a good tactic against an enemy Protector, for example, which relies on its energy supply to spam its repair beam.
And thirdly, to PREVENT the enemy from REPAIRING at Forward and Home Bases! The repair effect of FOB's and home bases will only initiate if the ship is not currently taking any damage. While fighters or bombers are harassing a ship, it will not repair. This is very useful against retreating enemy ships if you are pushing towards their FOB.

Bombers are used much the same way as fighters, with the exception that they cannot target other enemy squadrons. Ships only. They deal significantly more damage than fighters, and thus add a legitimate amount of firepower to a ships arsenal.
They are good for taking out a damaged foe who has ducked into cover to make a jump. They are not fast though, so you will have to watch the flow of battle and pre-empt moves such as this.
Your bomber squadron is highly susceptible to enemy fighter squads. If you see they have been engaged by enemy fighters, retrieve them immediately.

There are a wide variety of drones, each with distinct abilties.
I will explain them under two categories: support and offence

SUPPORT DRONES
Support drones' only function is to assist, heal, and buff yourself and your allies.
Here's what you'll see in the game...

Heal Drones
The Disruptor's heal drones are an example that requires attention when it comes to managing them in order to make the most of their ability.
They will heal you, and your allies, ALOT. It is difficult to take out a ship while it is being repaired by heal drones.
It is VERY important to retrieve them if they are not being used because, like all squadrons (with the exception of one), they have a limited flight duration, and a cooldown after docking (or death), and you want them to be ready when you DO need them.
Once they have fully healed an ally, look around to see if anyone else needs healing. These drones are very quick, teleporting to their target, so don't worry about where they are on the map.
This is great for jumping into a sector to heal an ally who's under attack on the other side of the map, if they are pushing the FOB for example.
Once every ally on your map is healed, retrieve the drones to capitalise on the cooldown so they'll be ready for the next skirmish.

Tugboat Drones
The Superflifter's tugboat drones, uniquely, have an unlimited flight duration. They'll increase the speed an ally by 20%, or yourself by 10%. Great for ferrying. Making sure your tugboat drones are on an ally at all times will reward you significantly with support points.
Tugboat drones will only work on cloakers while they are UNcloaked. If they cloak, the drones will return to you. I suggest giving them to the Brawler or Colossus. ;)
However, they die VERY easily. If the ally you have them on is about to be destroyed, retrieve them, otherwise the blast will wipe them out, and the cooldown on a new squad is 120 seconds.

Defense Drones
The Paladin's defense drones provide a 30% damage reduction. But their flight duration is extremely low, so timing is essential.


OFFENSE DRONES
Offensive drones usually nerf the enemy, making them easier to kill, and are usually designed to work in tandem with the parent ship's other abilities.

Slow Drones/Plasma Drones
The Colossus can choose between three squadrons in the loadout screen. Fighters, slow drones, and plasma drones. The slow drones give up damage output for an inhibiting affect on the targets flight model, making them slower. This is great for getting the Colossus in closer where it does more damage. The plasma drones will apply the plasma affect to a target for the length of their flight duration, but are more vulnerable to PDS.

Spotter Drones
Some ships, like the Hunter, Guardian, and the Watchman, have spotting drones. These basically make the target visible on your radar no matter where they are. Great for planning the Hunter's blinks, and the Watchman's or Guardian's aim.

Syphon Drones
These belong both to the Hunter and the Protector. They drain energy from their target, and give it to their parent. Great for keeping up those blinks and detects, or heal beams, while slowly reducing the targets abilities.

Ion Drones
Unique to the Infiltrator, they do a little damage, like fighters, but gradually stack 'ion charges' on the enemy, which increases the damage output from the Infiltrators ion blast.
The ion drones probably have the highest survival rate and cooldown than any other drone in the game. You can't really waste them.

Every squadron's worst enemy is the Colossus' flak cannon.
It rips them to shreds. You may want to think twice about sending your support drones to an ally who is under fire from a Colossus.

Another formidable enemy is the Paladin. It's plasma field weapon is an AOE around the ship, which dissolves any squadron on its ass. Combined with PDS, it's as deadly as the Colossus' flak cannon. I do not recommend sending a squadron of any sort against a Paladin, unless it has low energy.

The Pioneer, like the Colossus, has a main weapon with a small AOE which is deadly against squadrons. If a Pioneer is attacking you or an ally, think about retrieving your support drones.

Four ships have a small AOE ability that detects, scans, or buffs/heals itself, which will also damage squadrons. Those abilities are the:
Hunter's detect pulse
Venturer's heal/defend pulse
Disruptor's detect/slow pulse
Ranger's detect/slow pulse

Another thing that will make short work of your squadrons is combined PDS from 2 or more enemy ships. It's better to pick isolated targets.

Commander Air Group crew members!
If one of the main features of your ship are the squadron(s) it uses, you may as well take a CAG crew member. That will increase their flight duration, survivability, and cooldown.
For example, for the Disruptor I take Matilda Isaacs, who offers a 20% increase on the heal drones flight duration, giving you more time to heal your allies before they redock and cooldown.

The Zarek Paragon has been out of the hangar for a while now. Needed some balancing. But its re-release is imminent.
It will be the only ship, so far, with multiple squadrons at its disposal. Take heed. ;)
(edit: apparently the Paragon will not be the only carrier! There's allegedly a Titan Defense Systems carrier in the works!)