Freighters

In stock it doesn't make a whole lot of sense to use freighters. In the Balance Mod, it's worthwhile because of the expanded items that count towards cargo requirements and the fact they cost 50% less to maintain.

Space Empires Depot | SE:V Balance Mod

I use freighters as Planet Capture ships: load them up with troops, and use them to drop the troops.

Also, if your empire has several races, transporting races to worlds with the right atmosphere means you don't have to get that Planet Improvement tech and wait 50 turns in order to lose the domes on your colonies.

In Balance Mod however, they are much more useful. Ordinance, Supplies, resource harvest, Shipyards, and Repair Bays are all "Cargo" for the requirements, so I often use several designs rather than just the one. In my current game I have:

Mobile shipyards (for building Bases on Wormholes: the best border defense I've found)
Repair ships
Remote Resource Harvesters
Population Transport

all using the Freighter Hull.

I used them early for planet capture, then built cruser, and larger, planet assult craft, more shield and armor...
Nor my freighters are for pop movement, or getting troops and fighters from the back planet to the front line(s)...

I use frieghter hulls. But only for that... hauling freight. They have no combat value and only enough armour to survive passing through bad storms or asteroids.
I use them mostly to set up mine fields, transport populations around and to hold extra troops to replenish my landing craft.

Maybe I'm using them wrong, but I use them to transport supplies and ammo, mostly. When my fleets are a few systems away from supply lines and my new colonies haven't started to produce supplies yet, I find freighters to be great. I'm using the Balance Mod, by the way.

This is stock. You can't add Supply and ammo to freighters and have it count toward cargo. Freighters are a bit more useful in BM. However i like using combat hulls for supply ships anyways cause they can go faster and keep up with my fleets.

A minesweeper implemented on a medium hull can sweep 100 mines at a time in BM with level 1 mine tech. That's pretty useful. Of course this is with BM where the sweeping capacity of each component is greatly reduced from stock (as I recall).

I sometimes use them for a multi-purpose transport ship, having drone, mine, satellite and fighter launching capacity, plus cargo bays.
Handy when you need a generalized transport, but not enough needs to require building/maintaining more specialized ships.

Large frieghters also make handy super sized colony ships.
With thousands of kt of cargo space, and possibly even a few fighter/sat bays, they can not only carry defenses for the colony it will make, it can also unload sats/fighters into space should it get ambushed or otherwise run into enemies.

Another alternitive is a very flexible colony ship, a large frieghter with one of each colony type, plus a cargo pod, sat bay and fighter bay. It has a lot less cargo space, and cannot deploy units fast, but in some situations, such flexibility is handy, such as travelling several systems to a rock planet just to find someone else got there first and only ice and gas planets remain in prime territory.

Oh, can't forget scattering armor or the one scanner jammer, to prevent someone from figuring out what a freighter has ahead of time, could just be hauling sats, it could be a mine layer, or maybe it has a lot of drones or kamikaze fighters ready to cause havoc on the first enemy system they can be deployed into... or simply be empty and just out there to be a decoy...

Also, cloaked freighters, or cloaked super sized colony ships.
Establishing a colony in the middle of nowhere, after going 'through' hostile territory, can be handy, be it for recon, a stepping stone for further expanson, or simply to cause the local warmonger to have to plow through another empire to take out the rest of your colonies.