The Conquest is assuredly my favorite vanilla ship, hands down. In general I love expansion tech, but something about the Conquest appeals to me in every way.
I think a large part of my love for it is that the stock "Elite" variant is so atrocious (front torpedoes on a broadside fighting ship!? what?!)
Mine is similar to what someone mentioned earlier, though it took a ton of trial and error to find a variant that fits, and LORD does it fit. A storm needler, two heavy maulers, and a hephaestus assault gun on each side, burst PD lasers all over, with two MIRVs on front and two Sabot SRM pods on the side. I leverage my maneuverability and speed at long range with an Integrated Targetting unit, and cut a swath in any fleet.
If I get anything bigger than a Conquest like an Onslaught, I let the AI handle it. I'm too attached to it. But before the Conquest I'll generally helm my biggest ship, be it an Eagle or whatever. And anything I fly needs to be fit for Assault.