My ship would be the Infinite Discovery, a city-sized Titan class spaceship. It would have a dock that could house 100 small starships. In terms of weapons, it'd have dozens of plasma cannons, MACs(Magnetic Accelerator Cannons), four Orion nuclear missiles with a payload of 2500 megatons each (equivalent of a small asteroid), a dozen smaller Avalon nukes with multiple warheads, and a self-destruct mechanism that would yeild an explosion the size of Earth's moon. For defense, it would have invisiblity, hyperdrive, 1000's of EMP charges placed strategically on the ship's underbelly and sides, and enough armor to withstand a crash into Earth, with titanium alloys as thick as 30 meters in some places. There would be energy shields on every inch of the ship (except the cannons and missile chambers when they were open). It wouldn't have the most powerful engines because of the hyperdrive capability, but when would the Infinite Discovery every need to run away? A population of at least a million would live and work in the Infinite Discovery, and we would travel from planet to planet, moon to moon, galaxy to galaxy searching for life and resources.
Let me specify about my Orion nukes. They would not use their own propulsion to be shot at the target. Several specifically placed pulses of energy would sent them hurtling at a target. Since they would have to be in Earth's atmosphere to explode, they would first bore into the target's shell, and then explode. But let's say you have energy shields? The Orions are as big as a house, and come equipped with several hundred small EMPs. Once the Orion's inside, it'd explode. If you're in the ship, you have no chance. All the oxygen would be lit on fire (if it wasn't sucked out into space when the Orion peirced the ship's armor) and the ship would get shelled. All the systems and people would die, but the explosion couldn't completely destroy the whole hull (depending on how big your ship is). If I may make a comparison - imagine you're in a heavily-armored truck. Explosions on the outside couldn't damage you, but someone drills a hole into your door and drops a grenade into your cabin. Multiply the force of the grenade by about a billion and the size of the truck by about a quadrillion and it fits nicely. The smaller Avalons work the same way, but the one's on my ship are modified. They basically work the same way, except, of course, that they're smaller, and they don't drill into your ship. Once the Avalon's in range, it releases the modified warhead. Each is equipped with an EMP charge, and each attaches to a structurally critical part of ship, blowing the armor to shreds. Let me digress for a second. If I actually had to use the Orions or Avalons, I'm already in deep trouble. That means my MACs and plasma cannons haven't destroyed you. It probably means you're a worthy opponent.
Just thought of something! When my Orion missiles get within 1000 meters of your ship, they would be programmed to automatically hack your ship's sound systems and play Beethoven's Fifth Symphony out of all of the speakers. Mwahahaha!