In v0.6, due to CR and battle formats, I have two flagships I swap in and out of.
For normal, non-pursuit battles, when I do not use a frigate swarm, I use this:
Odyssey-class battlecruiser
Weapons: Plasma Cannon x2, Autopulse Laser, Burst PD x9, Harpoon MRM (Single) x3
Hullmods: Auxiliary Thrusters, Front Shield Emitter, Integrated Targeting Unit, Resistant Flux Conduits, Unstable Injector
Capacitors: 9
Vents: 50
This is my ideal configuration with max Combat and Technology. With less OP, I remove the capacitors, use fewer vents (no less than 30) and/or remove Resistant Flux Conduits, and I may remove a couple burst PDs, and swap out the plasma cannons for more autopulse lasers and Expanded Magazines.
I have adapted my configuration to not use Augmented Engines since engine hullmods may be mutually exclusive in the next patch.
For pursuits, or any battle when my fleet is a frigate swarm, I use this:
Hyperion-class frigate
Weapons: Heavy Blaster x2, IR Pulse Laser x2, Harpoon MRM (Single) x2
Hullmods: Accelerated Shields, Extended Shields, Flux Coil Adjunct, Resistant Flux Conduits
Capacitors: 18
Vents: 10
Again, assuming max Combat and Technology. The IR Pulse Lasers are for anti-fighter. Blasters are the strike weapons for everything else. With less OP, I take out the Flux Coil, and if my flux builds up too fast, I may swap out IR Pulse Lasers for Burst PD Lasers.
In any case, if I do not have the Optimized Assembly perk, which makes single Harpoons free to install, I do not use them.