Also, they give you the best burst damage. All torpedoes deal less damage against shields, so if you use torpedoes with a higher firing rate, most of the potential damage is wasted anyway. But since Quantum Torpedoes don#t fire that often, it's more convenient to time them the moment the enemy doesn't have shield and get the most out of their damage potential. That's also why I think Transphasics are fundamentally "wrong" and ineffective - they have even lower cooldowns, making it even more likely you would time the few shots you get off to hit hull, not shields, but their deal less damage and their special ability only is useful when you don't want to use them anyway.
Chronitons aren't bad, either, since they slown down your enemy, making it more difficult for him to get after you, run away, and making him more suspectible to damage.
Tri-Cobalts are great for their burst damage, too.
Photons if you fly a ship that can keepthem on target all the time, so their shorter cooldown times translate directly into DPS.
Quantums if you have a slower turning ship so you have to make each hit count for more.
Cronitons to slow enemies down, not particular useful in pve.
Tricobalt if you want the mega bang and can live with its horrendous cooldown and them been shotdown on occasion. More of a sniping tool.
Transphasics are crap, pure and simple, a quantum does more hull damage through a shield then a transphasic with the added bleedthrough.
Plasma is a sort of middle ground, and general not worth it either.