Just to note - My end-game setup is usually a star cruiser mounting dual huge weapons, usually that constant beam, forget what it's called. Particle beam? Then mounting two smaller energy drain lasers, and it seems like there's room for a few boosters in there too, can't quite recall... Get DPS there is enormous, and constant. With certain level of reactor tech, you can get constant fire on stations and deal fuckmassive damage. I'd be dropping top-teched security stations in like 4 seconds flat.
I seemed to use the carrier a lot too, replace the missiles with boosters and mount some cannons, energy leech, and that ion shotgun on a turret. You can stop ships dead with ion and then turn to ion them into oblivion.
Oh, and bombs totally rule. I use them a lot, you can one-shot whole groups of smaller ships if you work it just right. Against larger ships, you can utterly shred them, especially the ion bomb is like a godsend tackle, takes anything and reduces it to a floating husk for a good 30 seconds. Follow up with any weapon, it doesn't matter because they've got no shields and can't move. They work like massive nukes if you can control them right. Also a FANTASTIC way to farm freighters off civvie bases. Bomb them as soon as they show up, it slows, might drop shields, might even drop armor some, but more importantly it makes the AI swerve off-course, giving you a lot more time to deal damage.