energy guns (the chances for each is 2.5 % i think):
-phaser has a chance to disable one subsystem
-disruper has a chance to debuff targets dmg resistance marginally
-tetryon has a chance to to drain energy from all shield facings (just like tachyon beam)
-polaron has a chance to drain 25 energy from all subsystems
-antiproton has a chance to buff your damage (it has a critical bonus or something like that, im not sure though)
-photon has afaik no special tricks, just the highest dps
-quantum is just like photon but has higher actual damage but less dps (due to longer reaload, so its good for burst)
-chroniton slows the speed of your target and debuffs it's turnrate
-transphasic has a chance to ignore shields but i think its quite rare and it has the lowest dps
-tricobald has an enormous cooldown but is the only torpedo that does AoE and it's actual dps surpasses the quantum's by far
you can choose the weapons with the abilities you deem most useful/fun, i don't think there is one "musthave" weapon type...
edit: regarding carrying over skills: if you have basic skills like cannon upgrade or energy weapon upgrade (those are the skills to the left of your skill tree) then yes, they affect all cannon weapons. they are least effective but they apply to many guns.
then there are the specializing skills like disrupter or tetryon upgrades. as the name implies those skills only affect tetryon or disrupter guns respectively and do not apply to any other gun!