Photon torpedo

Photon torpedoes are secondary missile weapons used by the starships of the United Federation of Planets. They do damage via the release of gamma rays from a matter-antimatter reaction.

Quantum Torpedoes

Quantum torpedoes are more advanced in some way than Photon Torpedos. They involve discrete packets of energy (Quanta) in some way(citation needed). In all other respects, they are functionally Photon Torpedoes with a different color glow. Fewer events use Quantum Torpedoes so hard calcs are difficult to come by.

Transphasic Torpedoes

Only seen once, the Transphasic Torpedo is apparently able to pass through enemy shields and perhaps even phase through the hull of enemy ships. These weapons remain an almost complete mystery, except for the obvious fact that they do a very good job of destroying Borg Cubes. These cubes can be relatively easily destroyed through attacks to 'weak points', so this is the most conservative explanation for their effects.