Several games ago, I started building fighter factories for the early (conventional start) game. I didn't want to wait until Box Launcher tech and suddenly start building fighter factories because I finally had a tech to make them worthwhile. I decided I wanted to build up fighters for a variety of purposes, so that when I developed whatever killer techs worked with fighters, I would already have the fighter factories to exploit it.
First, I make jump scout pinnaces. They give me a huge jump from when I develop the basic jump engine techs to when an exploration ship can probe the jump points. Instead of researching a large jump engine, and retooling an existing shipyard, (or the drain of maintaining an untooled shipyard in anticipation of building a jump capable ship), I just build jump pinnaces and probe with them.
Also, fighter scouts can be very effective. You don't need that many HS of sensors if you can get your scout relatively close to an enemy without being detected. And because they operate from a mother ship, they don't need strategic range. They can go with the highest boost engine tech available. They can have an engine ratio that would be ridiculous for an armed ship, but is quite useful in a scout fighter. Because you don't need to retool, you can have lots of one off designs. (Although typically, I have at least 2 of each sensor fighter, so that I have redundancy if one gets eaten, or so the home planet and expedition force have equal sensor capability).
You can also use fighters for modular capability. Don't want the enemy to have any idea which ship is your flagship? Have all your slowish missile capital ships have a single hangar, and plop a flag bridge fighter pod in one, and pods with 9 HS sensors in others. Sensors work on ships or fighters that are in a hangar.
The fighter logistics vessel is a very nice tool indeed. It may be a bit of an exploit, as you get a LOT of maintenance supplies MUCH cheaper than if you had built the maintenance supplies with industry.
