I'm at mid-game on my current one.
Cap: 1x Odyssey (1x Dagger wing), 1x Heron (2x Gladius, 1x Longbow wing)
Destroyer: 2x Medusa; identical layouts w/ ATG, AWM, Stabilized shields, except one has pulse lasers and the other has phase lances. My officers are in these.
Frigate: 1x Scarab, 1x Tempest, 2x Hound (A), 1x Mudskipper Mk.II
Civilian: 2x Dram, 2x Buffalo, 1x Mudskipper, 1x Salvage Rig
Finally got enough rep to buy an Odyssey and found a TT station selling plasma cannons. Got the full broadside with two of those + 5 tac lasers. Since Tachyon is shit now, I took ITU instead. Obviously it's way too slow to use against any fleet not carrying at least cruisers (or massive swarms of smaller ships to kill), but the plasma cannons with the energy overcharge special ability are absolutely brutal when there's stuff you can catch. I really need to find/steal/buy a larger freighter though, I haven't been able to go far since I bought it.
Most other engagements I run in the Scarab, I've got it set with tac lasers, AM blasters, and four Hammer torpedoes, which is pretty much the sort of thing you want when you're running a small ship in a fleet: long-range delaying power and massive burst to break shields/shatter armor. Thankfully the Advanced Turret Gyros + Armored Weapon Mounts combo is still excellent.
The Mudskipper Mk.II I just happened across, I haven't fixed all the negative mods, but I already had a Hellbore ready to go for it. More of a show piece that I think is cool, I'm not sure how practical it is.