What are your favourites?
I kind of enjoy flying in heavily armed bombers - Ursa, Zeus - even though their turn rate is horrible, the shields are good enough for me, their payload is superior to any other craft, and they have multiple forwrard cannons (as well as a turret). As for the weapons - Mekhu HL-7. Sure, Maxim and Prometheus are powerful, Flail hits hard, Leech kills shields, but I find Mekhu's balance between damage, fire rate and energy drain just right for my skill :)

I like Myrmidons. Agile with good firepower. I'm liking the improved version of the Subach more and more, they have a rate of fire faster than the prometheous. The Maxim cannon is also really fun, mostly 'cause it shakes your cockpit while you fire.
As for missiles, the Tornado and Harpoon are usually my standards if its just a regular mission.
Erinyes are of course great, but you don't get those too often.

I prefer the Valkyrie. It has the best gun setup (close to the centerline with tight grouping so you don't have to compensate compared to the target reticle) compared to any other ship, it makes shooting a charm, and it has the legs to get anywhere in time.

For fighters, the Ares is my choice. A ton of armour, near-bottomless missile banks and a massive powerplant to keep the guns running, yet also (barely) able to dogfight. Just... don't use it if you need to go anywhere in a hurry. Well, anywhere at all really, hurry or not. And yes, this did come back to haunt me in a certain mission :P
When flying a bomber, I'll have to go with a Vasudan though. The Sekhmet rules all.
Guns? I'd pick Kaysers over anything else if I'm flying a ship with a good energy recharge, ideally paired with a Maxim in a second bank for dealing with cruisers at range. When not in a ship that can sustain these hungry weapons though, it's either the good old Subach (that thing never gets obsolete) or the Prometheus S.
Finally, missiles - The Tempest dumbfire missiles are one of my first choices, followed by Trebuchets for interception or Harpoons for dogfights. Tornado is also a good pick but I always seem to go through them so fast.... guess I'm a bit trigger happy :)