For light ballistics, excluding bomb bay, my pick would be light needler. It is good, but too overpriced. Anytime I consider light needler, I want railgun instead every time. Light Needler needs its 800 range from pre-0.9a releases back! As for light autocannon, it is not that bad, but it is overpriced for what it does. Make it 3 OP and it would be more useful. If dual light machine guns were not useful for some niche builds like SO berserkers, that probably would have been my pick for worst light ballistic. 5 OP seems too much for a minor DPS boost over the cheap light machine gun.
I mentioned 700 range as the reason Storm Needler is the worst heavy ballistic. With 700 range, any AI ships that have it need Aggressive AI to use it effectively, while other heavy weapons can get by with Steady. I tried Conquest loadouts with various combinations of weapons, some with Storm Needler and others without. They all kill the enemy at about the same time, so why would I want to be dragged closer to Storm Needler range when I can pop enemies from further away with 800 to 900 range ballistics?
Mining blaster is sub-par, but it is a great armor cracker for starter Apogee against weaker battlestations it can solo. Early game, if I find Locusts first, I prioritize it over the large energy mount, and will keep mining blaster as an armor cracker until I find Plasma Cannon. Mining Blaster is probably the best weapon Hyperion can use, but Hyperion is sub-par in 0.9a.
Heavy burst PD is bad because it is merely a burst PD with a bit more range and charges at significantly more flux and OP costs. If not for Ion Pulser, heavy burst PD would be my pick. At the range Ion Pulser is effective, non high-tech ships with SO can simply kill the enemy quickly instead with HMGs and chainguns. Why cripple the enemy instead of killing it?
As for small missile, if I had to pick one, it would be small Atropos, and only because 2 OP costs too much for it. It may be too cheap at 1 OP, but 2 OP is too much. Atropos would be good at 1200 damage, but I think Alex mentioned that was too strong on Daggers. Stupid Daggers ruining Atropos for playership use!
If there were more ships that could use Hammer Barrage and Cyclone Reaper effectively, my choice for worst large missile would be Squalls. Low ammo, horrible tracking, less effective than Sabots at overloading ships. But, with the current ships, dumb-fire anything are the worst because no ship aside from Legion (XIV) can use them effectively or survive contact with the enemy. I suppose suicide berserker disposable Gryphon could work. Maybe next release, Radiant for those with Automated Ships can use them as wingmen, but that relies on player getting a certain level 5 tech skill (and player cannot pilot Radiant). Hammer Barrage has low ammo, but player can dump the whole clip fast and destroy whatever is in front of it quickly. (Cyclone Reaper takes ages to reload, and Reapers are too fragile without Missile Spec.) If Hammer Barrage had more ammo or less OP cost, it would be good, provided it had good ships to use them, which there are not today aside from Legion (XIV).
If that weren't the case I could see myself using a Odyssey build with Paladins or a PD Onslaught as you mentioned.
Paladin would be no good because its flux cost is too high. I tried Paladin on Paragon as an alternative autopulse, but the flux cost is high enough to overload Paragon.
I have used beam PD on Falcon or Eagle at times because their energy mounts are set so far back, and they rely mostly on ballistics for damage.
Large Missile: Nothing here is terribly bad but Hammer Barrage is obviously the weakest of all, makes sense since it's available on open market but it usually misses most targets (it's like a Hurricane MIRV but inverted) unless you're point blank. Fast daamage but it kinda runs out quickly, which is ok I guess since mostly Ludds and Pirates use it.
Radiants too, and they are nasty.
P.S. Come to think of it, maybe 1 OP is not too cheap on Atropos. It cannot be used point-blank like Harpoons because of the arming delay, and the range is much worse. Atropos trades range and point-black use for slightly better stats than Harpoon. Maybe it would compete with one-shot Hammer, but that does 1500 damage instead of 1000.