For ballistic mounts, it varies by ship.
For Dominator, I use Vulcans (and IPDAI) because I usually want to use assault weapons instead of flak in the medium mounts. I may put two railguns in the rear to defend against smaller ships and missiles. I find IPDAI necessary for small weapons to track well enough. (I tried no IDPAI, and Vulcans alone were unreliable.)
Eradicator probably gets Railguns and Ballistic Rangefinder.
For Onslaught, I leave them empty. I tried Ballistic Rangefinder and Railguns on Onslaught, but they tend to get knocked out frequently under enemy fire. Heavy weapons are more resilient against knockout from enemy fire.
For Legion, sometimes, I mount Mortars, Vulcan, or Railguns, or leave them empty, depending on other weapons.
Atlas II is empty. It needs all the OP it can get for two Gauss cannons, two MIRVs, and the hullmods to support those weapons.
For small energy mounts (Conquest, Odyssey, Astral, Paragon), I try to fill them with burst PD or IPDAI IR Pulse Lasers (or Omega weapons if I have them), depending on what I need. The continuous beam PD is not strong enough. Note that IR Pulse Laser is efficient, and good for anti-fighter, especially with elite PD. Sometimes, I leave few of the mounts empty. I prefer to shoot down incoming missiles (and fighters and mines) before they put hard flux on the shield.
Notable ships:
Fury. If I have elite PD, I put an IR Pulse Laser or Ion Cannon to compliment the Heavy Blaster. Maybe a burst PD too. I use two burst PDs for the rear. The rest are empty. It seems many mounts are for continuous beam PD, not for the effective, more expensive weapons.
Champion. I tend to leave small mounts on the front empty. I think I put two in the rear
Conquest. I want some PD on it, and I mount at least eight burst PD. Occasionally (if I give it to an Aggressive+ officer), I may skip the PD and put Converted Hangar -> Xyphos on it instead.
Paragon. I put some burst PD for anti-missile.
Astral. If I have elite PD + IPDAI, I cram as many IR Pulse Lasers on it as I can get away with and let it rip against smaller ships that get too close.
Ziggurat. I like IR Pulse Laser plus IPDAI for additional PD when its motes are not available or not enough. (Motes alone is not enough against huge fighter swarms or Doom stacks and their mine spam.) If I want more burst damage instead, I may mount Antimatter Blasters instead. Of course, if I have Omega weapons (Rift weapons, AMSRMs), they get used instead.
P.S. More ships.
Doom. Light Needlers or AMBs.
Mora. Railguns and LAG in front mounts, Vulcan in side and rear mount. It has enough OP to act like a battlecarrier.
Heron. Burst PD (four of them), if I have elite PD skill. Here, they double as anti-armor to compliment its main gun. That said, I only use this if I have s-mods on Heron. Heron has too few OP to work as a battlecarrier without s-mods. (Heron needs that +10 OP boost that Mora got.)
Brilliant. Burst PD.
Radiant. None at the front, four IR Pulse Lasers in the rear against occasional attackers. Radiant is all about the bigger guns.