In reality fighters will probably be simple drones that have only as much a heat signature as the nearest star warms them up, and capital ships will have only a few people as crew, thus eliminating any fun that we have in FreeSpace- a fighter 'pilot' would program the flight of several wings and AI would take over.
Fighters would do a good job at intercepting guided warheads the enemy fires, and perhaps even railgun projectiles would be fired at with some intercepting missiles (a few kT could push a railgun projectile off it's path) or lasers. With a bunch of these orbiting capital ships it would be possible to intercept threats earlier. The fighters could also form a huge sensor array.
Bombers would be useful to try to flank enemy ships and attack from directions that there are no fighters, or assuming some form of "subspace" is discovered- they'd warp in too close to maneuver capital ships away from attacks, drop their payload, and hopefully warp out before the first nukes get shot down.
Cruisers would be bomb and strike craft killing units, perhaps with some serious sensors to pick up attackers through all the noise that the enemy task force would definitely be making to blind them. They'd also have to have a few meters of composite armor on their outer skin, and much more below to be able to absorb any kinetic energy rounds, and perhaps near misses from nukes, or moving through laser beams. In a world with subspace, expect these to warp in near an enemy task force to paint it with sensors, and probably also attack until out of missiles or energy for lasers.
The recoil of big Gauss guns would probably push these things around a bit, and the magnetic fields involved with firing the guns might pull people with metal buttons on their shirts across rooms, so I wouldn't expect too many cruisers to have them.
Destroyers would be big and slow. They'd need to be megaliths with caves dug deep within to hold the few crew members, reactors, weapons and strike craft. A mountain of 500 meters of titanium reinforced granite that is a couple kilometers long would be able to stand up to prolonged bombardment, and their main weapons would be bombers and swarm missiles to destroy the soft objects on enemy destroyers, such as sensors.
The big ships' engines would be hidden deep withing the hull, and all exhaust gasses would leave through caves hundreds of meters deep.
The capital ships would also use some serious Gauss guns, throwing projectiles that weigh as much as freight train locomotives at several times the speed of a geo-stationary satellite. While these would be interceptable, they'd be able to create serious cracks on the surface of enemy destroyers' hulls, and after prolonged bombardment- some serious damage, and perhaps destruction.
Then there's beam cannons- spitting out particles with so much energy that such granite mountains would quickly have part of them turn into a volcano erupting lava into space.
Now let's introduce shields- a system that has multiple very small jets on the hull of a ship. These jets throw plasma at anything that comes really close, similar to modern active armor throwing rockets or pellets. The very violent plasma discharge would be strong enough to negate the effect of incoming rounds, at least until the shield system would have enough energy to continue operating.
