Expanding on this thread, I thought I'd give my own thoughts on the use and strengths of the different weapons available in the game.
First off, the chance to proc secondary effects with these weapons seems to be extremely low for the most part. This is most likely the case due to the potentional for volume fire in a fleet setting. If one ship were capable of inflicting persistent debuffs on it's own, then a fleet would not only be able to achieve to the same, they'd be able to do it across the board using every damage type to inflict every effect indefiniently. This would make raiding during PVE or Events too easy.
As a result it's probably best to specialize not only on individual basis, but within a group to increase your chances of inflicting the desired debuff and making it stick.
Phasers have the distinction of inflcting multiple debuffs on a target. There's a chance to knock any of the four main subsystems offline for a split second. It may even be possible to knock all four systems off-line if you're extremely lucky. Potentionally the most dangerous and powerful with extreme volumes of fire, but greatly reduced effectivenss otherwise.
It's iconic status and compartively cheap cost in skill points will probably lead to it being a common damage, which may result in PVPers shield and hull hardening against this damage type specifically.
Perhaps the most practical damage type in a mass-fire setting. Adding 10% damage to an group could result in many thousands of additional damage points. Unfortunately, once you reach a certain point in volume fire, the proc stops yielding a benefit. Meaning that if you manage to keep the effect persistent, you'd be better off with any other damage type.
As with Phasers, Disruptors are something of an icon and are cheap to level up, but will probably only be slightly more common than other damage types amongst serious PVPers. Resist hardening may pay off, but then again, it may not.
Imo, the second best damage-type for personal use, while being the weakest in a group setting. Handy in that the proc lasts for a fairly long time and that it remains fairly strong even against a hardened target or when low power settings are used with an energy weapon. A faithful damage-type, but the chances of spectacular results are slim to none.
Due to the fact that it's weak in a pvp setting, you probably won't run into it that often. Of course, there's always the chance that someone may see that supposed weakness as a strength.
This one is harder to guage. Considering that disruptors do basically the same thing while also increasing damage to the hull, you'd have to wonder why you'd go with something that's only especially effective against shields while also costing more points to train. But then, you have to consider the fact that rather than a debuff that can not be stakced over time, it's a personal buff applied to each individual weapon per shot. It would be a very good damage type to have if there's a sufficiently large volume of disruptor fire already present.
Any well organized PVP or PVE group would do well to have this damage type, but only if Phasers or Disruptors are already available in sufficient quantities. As a practical matter though, this damage type won't be all that common at all.
Phasers are better if you have alot of phasers. It's probably stronger for personal use or wthin a smaller group setting though. People that like to tank would likely be comfortable with the resulst, since it can reduce energy attacks by 50% for a split second.
The strongest damage type for personal use. Good against both shields and hull, a buff rather than a debuff that cannot stack, If there are already many Disruptors and Phasers focusing on a target, this will allow you to become the King of Damage. Beware, it's the most expensive in terms of skill points and the weaponry will likely be very rare. You probably shouldn't train it, unless you have a weapon on hand.
In a PVP setting, it'll be the most advantageous damage-type to have, since not only will it be difficult to harden against it, but it'll be so uncommon no one would bother to do so even if they could.
Generally having a better chance to inflict a debuff where available, a much lower volume of fire with restrictive firing arcs, and all dealing the same damage type that is universally guarded against with standard shields, the flavor of a torpedo launcher has more to do with personal preference than min/maxing volume fire within a group setting. However, team work and organization can still be used to get the most out of your launchers.
Similiar enough in function to mention in the same breathe. For personal use, two Phontons is better than two Quantums, but three Quantums are better than three Photons. Assuming that you have alternative ways of bringing down a target's shields that is. Otherwise, go with Photons.
A debuff that does not stack with the plasma energy weapons, while having lower burst and dps than quantums, the real reason why you would pick this over all others is the High-Yield torpedo. Whether in a group setting or not, it's a good way to maximise the effectiveness of probably the singularly most powerful tactical ability in the game.
Good against heavily shielded targets, bad against targets with alot of hull points. You'd probably be better off just knocking down the shields, but that may not be as easy as it sounds.
A debuff that doesn't stack with itself. Probably only good in a PVP setting and only within a small group. Maybe if it effected turn-rates...?
Lowest DPS, highest burst, uncompatible with powers. It may be good on a ship with limited tactical abilities or a ship with multiple launchers, but otherwise you'd probably better give it a miss.
Mines have lower DPS than torpedoes, but can cause more burst damage. A large field may add up in in terms of damage. Personally, I think they should be cloaked so you can counter act cloaking devices during PVP. Fed ball, floating through space, dropping mines every where. Sooner or later, they'll have no where to go!