The DPS if the different wepon types is about the same, its just how they do that damage, so a plasma or chemical attack will do 1 large bit of damage followed by a few small ticks afterwards. EMP, Chemical and Plasma all do better damage to certian systems, such as reactor, hull and shields which has to be factored in. So althoguh the base is pretty much the same for all damage types, how they actual apply it is what differs, which can be a big deal depending what types of mobs you are fighting. For example, biological mobs have no hulls, so plasma is generally better to use on them for the bonus damage.
The other thing to look out for is the damage numbers when you are attacking a mob, some obs have partial resists to some damage types and some have full resists. I can't remember if it was Tengu or Voltoi that were completely immune to impact damage for example.
I'm not 100% sure, but I think it was either impact or energy that hada chance of interupting a mobs skills as well?