Weapons:
While each one of them should give a specific debuff, range and RoF to create different "weapons" but balanced in a whole so, for example:
Plasma hits for more in hull and armor less on shields;
Phaser has a long range but less effective on armor;
Polaron hits more and has longer range but costs more flux;
Phased Polaron hits the same but has better RoF meaning more flux cost;
Retrodit Phaser same as a normal phaser but hits for less;
Antiproton very high RoF but costs more Flux;
Tetryon has the longer range but lower RoF;
Disruptor hits shields for more but lower on hull and armor;
Polarized Tetryon has the longest range but even lower RoF;
Plasma-Disruptor Hybrid hits for more both Shields and Hull but has a lower range;

Mix on those 2 colors (Plasma and Disruptor)
Spiral Wave Disruptor Has higher damage versus shield, same range as a Phaser but has the lowest RoF.

Plus a Disruptor "aura" color
Energy:Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton, Retrofit Phaser, Plasma-Disruptor Hybrid, Polarized Tetryon, Spiral Wave Disruptor, Phased Polaron (Beam Array (Hardpoint) 180°, Small); <- note:
Fighters have these as well with a 360º but lower damage.Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton (Turret (Turret) 360°, Small and lowest damage);
Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton, Polarized Tetryon (Beam Banks (Hardpoint) 90º, Medium, while hitting less compared to cannons, it always hits);
Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton (Cannon (Turret) 90º, Medium, note: cannons are projectile types, meaning they hit harder but have a chance to miss);
Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton, Phased Polaron (Dual Cannon (Turret) 90º, Medium);
Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton, Polarized Tetryon (Dual Beam Banks (Hardpoint) 90º, Medium);
Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton, Plasma-Disruptor Hybrid (Dual Heavy Cannon (Turret) 45º, Large);
Phaser, Disruptor (Quad Cannon (Turret) 45º, Large, note: because of the OP and Flux cost, they can only be used on the largest ships. );
//if Theres a way to make them untargetable as missiles then these should be missiles, else, just make them into Ballistic guns
Photon, Quantum, Plasma, Transphasic, Chroniton, Tricobalt, Hargh'peng, Rapid Transphasic, Chroniton Flux (Torpedo Launcher (Hardpoint) 90°, Low shield damage, very high armor/hull damage)
Missile:Tricobalt Torpedo Launcher (Hardpoint) 10°, very high damage, Slow and targetable.
All info was based on Star Trek Online.So what Factions uses what
Phaser <- Federation, Terran Empire and also Cardassian Union
Disruptor <- Klingon Empire, Orion Syndicate, Breen, Romulan, Reman and Gorn Hegemony
Polaron <- Dominion
Plasma <- Borg (Special type of Plasma weapons)
Antiproton <- Undine, Iconian (Undine and Iconian have a Special type of Antiproton (the Undine have a yellow like beam and the Iconian have a purple beam, the Iconian have the strongest hitting beams in the game)
Spiral Wave Disruptor <- Cardassian Union