All weapons of the same mark and quality have the same base damage. The difference is in the proc, or special effect, each type has. Each has a 2.5% of causing the following effect:
Phaser: disables a random subsystem
Disruptor: lowers targets damage resistance
Tetryon: additional shield damage
Plasma :additional damage over time to the hull
Polaron: lowers all power levels
Antiproton: additional Critical damage.
Photon: your basic torpedo, goes boom
Quantum: fires more slowly than photon, but does more damage per hit. Good for high yield strikes
Plasma: Additional hull damage over time.
Transphasic : increased shield penetration
Chroniton: slows the target by 2/3 for a short time
PvP players tend to use disruptor and antiproton mostly, for the slight edge in damage due to their procs. Plasma seems to do the most damage in PvE, but are tend to be the least effective in PVP, due to most of the high end gear's resistance to plasma damage.