Want more torps to fire? Go photon. They have faster recharge that a quantum torpedo with comparable damage. You will get more DPS out of this.
Want some DoT damage with them? Go Plasma. This has a slow recharge and has a very weak initial hit. The key here is it applies a DoT 1 out of 3 shots. This DoT takes the total damage above the max from a photon torpedo.
Want high damage per shot? Go Quantum or Tricobalt. Quantums have about 8 second recharge and are good when you don't have the target in your sights for long. Think of a cruiser trying to turn to fire, or a escort in hit and run tactics. Tricobalt I think it is, has a very long recharge but a very powerful shot.
Want shield damage? Transphasic torpedos really damage shields, but not so much on the hull of a ship.
You have to balance recharge, cooldown, utility, and damage per shot. It all depends on your playstyle.
For instance, I zip around for hit and run tactics with my escort. My time on target (time target is in my sights) is low. Thus, I want to make the most of my time on the target. I went with quantum torpedo launchers. I use multiple high yield skills to get the most out of each shot. 2/3 of my shots are multiple torpedos. This provides me with some massive burst damage. Seeing 3 4k numbers pop up alongside my 400-600 damage cannon hits on a ship makes me smile for some reason =) 8 Seconds later I'm doing the same thing on another target, this time with only 2 4k numbers.
Browse around the forums some, there are some posts that describe the differences in more detail. This is more of a watered down version.
As the above poster mentioned, they all have the place.
But I also settled on the Quantum. It hits really really hard. I don't care about the slightly longer recharge time since I don't spam torps anyway. I wait till the shields are down and then launch. Quantums also travel pretty fast which is handy; otherwise, the targets shields might have partially repaired.