I use a variety of ships depending on the game and availability.
Planes: STEALTH FORCE IS GO. I almost always choose a planet with planes if possible. The ability to build a huge swarm of them in the opening minutes of the game thanks to low resource costs means you've more than likely cleared a handful of planets around you and an ally's home stations. This head start in the beginning, and judicious micromanagement of low power mode can equate to near lossless gate-raiding, or capturing a planet. You can also send them in ahead of a main force to take out wormhole defense without worrying about mines(exposing friendlies to less damage) and reaching key positions on a planet.
Munitions: Reminds me of finding the shot upgrades in the old arcade shooters. more boosters more power. As an individual unit, they are outclassed by a starship's boosting ability, but as a group of even 10 or so, the overlap assures me that every single one of my ships is running on at least one cup of caffiene at all times, like me.
ZBeam frigates: not too great alone, but move em in group-move with the rest of your fleet, and you effectively prevent the enemies from catching a long-enough breather to have an engineer heal it. Beam attacks SEEM to be instantaneous, so there is no chance of firing a volley and having an engie fix something in-between shots. Also, its orange attacks spice up my domination.
Viral shredders: BEST MELEE SHIP. PERIOD. Set these babies loose on FRD. If a shredder or group of shredders isn't doing mega-damage on something, no problem because they'll just make more, and eventually, that ship increase can start to add up. Admittedly, they begin to take a massive drain of energy, but..SCRAP em, and get resources from the AI(since AI provided BP for the ship(s) scrapped).
Parasites: So uh..instead of fighting me..let me make you an offer you CAN'T resist(unless immune to reclamation). Parasites aren't the strongest units, but I assure you, reclaiming engineers that are repairing wormhole defenses, lvl 3 and 4 enemy ships, and wandering patrols as you raid, is something worth mentioning. 5xxx-7xxx ships planning a CPA? Do you know where they're gonna strike? If so, send the Parasites to "Bargain" with your enemy. I don't destroy ADV factories or ADV labs, why destroy enemy ships when I can use them too?