Weapons:Plasma Normal range, Bonus damage on hull and armor less on shields, Normal RoF;
Phaser Long range, Normal damage, Normal RoF;
Polaron Normal range, Bonus damage on hull, Normal RoF;
Phased Polaron Longer range, Bonus damage on shields, Lower RoF;
Antiproton Normal Range, Melts Hull and Armor, Normal RoF;
Tetryon Normal range, More damage on Shields, Normal RoF;
Disruptor Lower range, More damage, Normal RoF;
Spiral Wave Disruptor Normal Range, More damage, Lower RoF.
Plus a Disruptor "aura" color
Energy:Beam Array: Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton, Retrofit Phaser, Plasma-Disruptor Hybrid, Polarized Tetryon, Spiral Wave Disruptor, Phased Polaron (Medium mount, MK 6 to 10);
Dual Beam Array: Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton, Polarized Tetryon (Medium mount, MK 6 to 10);
Ballistic:Cannon: Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton (Medium mount, MK 6 to 10);
Dual Cannon: Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton, Phased Polaron (Medium mount, MK 6 to 10);
Dual Heavy Cannons: Phaser, Disruptor, Plasma, Tetryon, Polaron, Antiproton, Plasma-Disruptor Hybrid (Large mount, MK 7 to 10);
Quad Cannons: Phaser, Disruptor (Large mount, Only MK 10 available);
NOTE: All MK 6 are Small mounts.Missile:Photon, Quantum, Plasma, Transphasic, Chroniton, Tricobalt, (Medium mount MK 6 to 10).
So what Factions uses what:
Phaser <- Federation and Terran Empire
Disruptor <- Klingon Empire, Orion Syndicate, Breen, Romulan, Reman and Gorn Hegemony
Polaron <- Dominion
Tetryon <- Tholian
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, the Iconian have the strongest hitting beams in the game)
Spiral Wave Disruptor <- Cardassian Union
All images are from Star Trek Online. Weapons are based on the series and Star Trek Online.