Below are a variety of ship loadouts I use for my 0.9.1a game, some for endgame, others for early game. Not all are fully optimized. Assumes Loadout Design since that skill is so good for everyone.
FRIGATES
Afflictor
Capacitors: 12
Vents: 12
Weapons: 4x Reaper Torpedo
Hullmods: Efficiency Overhaul, Expanded Missile Racks, Flux Coil Adjunct, Reinforced Bulkheads, Resistant Flux Conduits, Unstable Injector
Tempest
Capacitors: 9
Vents: 10
Weapons: 1x Heavy Blaster, 1x Tactical Laser, 1x Salamander MRM
Hullmods: Efficiency Overhaul, Hardened Subsystems, Integrated Targeting Unit, Resistant Flux Conduits
DESTROYERS
Hammerhead
Capacitors: 10
Vents: 24
Weapons: 2x Heavy Mortar, 2x Railgun, 2x Reaper Torpedo, 2x Vulcan Cannon
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Reinforced Bulkheads, Resistant Flux Conduits
Harbinger
Capacitors: 20
Vents: 13
Weapons: 3x Antimatter Blaster
Hullmods: Auxiliary Thruster, Efficiency Overhaul, Hardened Subsystems, Integrated Targeting Unit, Unstable Injector
Enforcer
Capacitors: 12
Vents: 24
Weapons: 1x Heavy Mortar, 2x Arbalest Cannon, 4x Annihilator Rocket Launchers, 2x Flak Cannon
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Reinforced Bulkheads, Resistant Flux Conduits
Medusa
Capacitors: 1
Vents: 24
Weapons: 1x Heavy Blaster, 1x Ion Beam, 2x Railgun, 3x Burst PD Laser
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Resistant Flux Conduits
Mule
Capacitors: 12
Vents: 20
Weapons: 1x Arbalest Cannon, 2x Salamander MRM, 2x Light Mortar, 1x Vulcan Cannon
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Reinforced Bulkheads, Resistant Flux Conduits
Shrike (P) (early)
Capacitors: 5
Vents: 18
Weapons: 1x Pulse Laser, 1x Sabot SRM Pod, 1x Ion Cannon, 1x Light Autocannon, 1x IR Pulse Laser, 2x PD Laser
Hullmods: Efficiency Overhaul, Reinforced Bulkheads
Shrike (P) (late)
Capacitors: 6
Vents: 20
Weapons: 1x Heavy Blaster, 1x Salamander MRM, 1x Railgun, 1x Tactical Laser, 2x PD Laser
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Resistant Flux Conduits
Sunder (assault)
Capacitors: 10
Vents: 24
Weapons: 1x Tachyon Lance, 2x Railgun, 1x Vulcan Cannon
Hullmods: Efficiency Overhaul, Hardened Shields, Integrated Targeting Unit, Resistant Flux Conduits, Stabilized Shields
Sunder (beam)
Capacitors: 1
Vents: 24
Weapons: 1x High Intensity Laser, 2x Graviton Beam, 2x Light Autocannon, 1x Vulcan Cannon
Hullmods: Advanced Optics, Efficiency Overhaul, Integrated Targeting Unit, Reinforced Bulkheads, Stabilized Shields
CRUISERS
Apogee
Capacitors: 7
Vents: 36
Weapons: 1x Plasma Cannon, 1x Locust SRM Launcher, 2x Pulse Laser, 2x IR Pulse Laser
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Resistant Flux Conduits
Aurora (missiles)
Capacitors: 0
Vents: 33
Weapons: 2x Heavy Blaster, 2x Sabot SRM Pod, 4x Sabot SRM Launcher, 5x Burst PD Laser
Hullmods: Efficiency Overhaul, Expanded Missile Racks, Integrated Targeting Unit, Resistant Flux Conduits
Aurora (energy)
Capacitors: 4
Vents: 36
Weapons: 2x Heavy Blaster, 1x Ion Pulser, 1x Salamander MRM Pod, 5x Burst PD Laser
Hullmods: Efficiency Overhaul, Hardened Shields, Integrated Targeting Unit, Resistant Flux Conduits, Shield Conversion: Front
Dominator
Capacitors: 9
Vents: 36
Weapons: 1x Hellbore Cannon, 1x Mark IX Autoncannon, 2x Flak Cannon, 3x Annihilator Rocket Pod, 9x Vulcan Cannon
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Reinforced Bulkheads, Resistant Flux Conduits
Notes: Disposable clunker loadout to throw at the enemy.
Doom
Capacitors: 30
Vents: 16
Weapons: 2x Heavy Blaster, 2x Salamander MRM Pod, 4x Burst PD Laser, 4x Light Mortar
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Resistant Flux Conduits
Notes: Could remove light mortars and lower vents to 9 for Hardened Subsystems instead.
Eagle #1
Capacitors: 0
Vents: 32
Weapons: 2x Heavy Needler, 1x Heavy Mauler, 3x LR PD Laser, 3x Graviton Beam, 2x Burst PD Laser, 2x Atropos Torpedo
Hullmods: Efficiency Overhaul, Integrated Point Defense AI, Integrated Targeting Unit
Eagle #2
Capacitors: 0
Vents: 30
Weapons: 2x Heavy Needler, 2x Phase Lance, 1x Ion Beam, 5x Burst PD Laser, 2x Atropos Torpedo
Hullmods: Advanced Optics, Efficiency Overhaul, Integrated Targeting Unit
Notes: Medium ballistic hardpoint is empty.
Falcon (early)
Capacitors: 0
Vents: 28
Weapons: 1x Arbalest Cannon, 1x Heavy Mortar, 2x LR PD Laser, 2x Graviton Beam, 2x Burst PD Laser, 2x Atropos Torpedo
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Reinforced Bulkheads, Resistant Flux Conduits
Falcon (late)
Capacitors: 0
Vents: 27
Weapons: 1x Hypervelocity Driver, 1x Heavy Mauler, 2x LR PD Laser, 2x Graviton Beam, 2x Burst PD Laser, 2x Atropos Torpedo
Hullmods: Efficiency Overhaul, Integrated Targeting Unit, Reinforced Bulkheads
Heron (cheap)
Capacitors: 6
Vents: 18
Fighters: 1x Khopesh, 1x Broadsword, 1x Talon
Weapons: 1x Heavy Blaster, 6x LR PD Laser
Hullmods: Efficiency Overhaul, Reinforced Bulkheads
Heron (late)
Capacitors: 5
Vents: 17
Fighters: 3x Sparks
Weapons: 1x Heavy Blaster, 4x Burst PD Laser
Hullmods: Efficiency Overhaul, Reinforced Bulkheads
Mora
Capacitors: 8
Vents: 27
Fighters: 1x Khopesh, 1x Broadsword, 1x Talon
Weapons: 2x Hammer Torpedo, 3x Vulcan Cannon, 3x Light Mortar, 2x Light Autocannon
Hullmods: Efficiency Overhaul, Reinforced Bulkheads, Surveying Equipment
CAPITALS
Astral
Capacitors: 0
Vents: 18
Fighters: 1x Dagger, 2x Cobra, 1x Khopesh, 2x Longbow
Weapons: 5x Heavy Burst Laser, 2x Salamander MRM Pod
Hullmods: Augmented Drive Field, Efficiency Overhaul, Expanded Deck Crew
Conquest #1
Capacitors: 5
Vents: 60
Weapons: 2x Mjolnir, 2x Marx IX Autocannon, 2x Heavy Needler, 2x Locust SRM Launcher, 8x Burst PD Laser
Hullmods: Efficiency Overhaul, Expanded Missile Racks, Hardened Shields, Integrated Targeting Unit, Resistant Flux Conduits
Notes: Symmetrical loadout that Steady AI can use, with Mjolnir, Heavy Needler, and Mark IX together. One medium ballistic mount per side is empty due to range mismatch between the large and mediums. (800 range on back mount might not be long enough, and 1000 range might mess up the other three.) Excess OP goes to Expanded Missile Racks so that Locusts last long enough.
Conquest #2
Capacitors: 9
Vents: 60
Weapons: 4x Storm Needler, 4x Heavy Mortar, 2x Locust SRM Launcher, 8x Burst PD Laser
Hullmods: Efficiency Overhaul, Hardened Shields, Integrated Targeting Unit, Resistant Flux Conduits
Notes: If given to AI, must be given Aggressive officer/AI for it to get close enough to use Storm Needlers.
Legion
Capacitors: 0
Vents: 51
Fighters: 1x Khopesh, 1x Claw, 1x Broadsword, 1x Wasp
Weapons: 2x Hellbore Cannon, 2x Heavy Needler, 3x Dual Flak Cannon, 6x Vulcan Cannon
Hullmods: Augmented Drive Field, Efficiency Overhaul, Integrated Targeting Unit
Odyssey
Capacitors: 0
Vents: 40
Fighters: 1x Xyphos, 1x Mining Pod
Weapons: 2x Plasma Cannon, 1x Hurricane MIRV Launcher, 3x Salamander SRM, 11x PD Laser
Hullmods: Efficiency Overhaul, Hardened Shields, Integrated Point Defense AI, Integrated Targeting Unit, Resistant Flux Conduits
Paragon
Capacitors: 0
Vents: 55
Weapons: 4x Tachyon Lance, 2x Hypervelocity Driver, 4x Heavy Blaster, 9x Burst PD Laser
Hullmods: Augmented Drive Field, Efficiency Overhaul, Hardened Shields, Resistant Flux Conduits, Stabilized Shields
Onslaught
Capacitors: 0
Vents: 51
Weapons: 2x Devastator Cannon, 1x Mjolnir Cannon, 4x Heavy Needler, 2x Hypervelocity Driver, 3x Dual Flak Cannon, 6x Vulcan Cannon, 4x Typhoon Reaper Launcher
Hullmods: Augmented Drive Field, Efficiency Overhaul, Integrated Targeting Unit, Resistant Flux Conduits
Notes: Typhoons instead of Annihilators because AI will empty the latter very quickly. At least AI conserves Reapers. Defense is a bit weak on the sides.