Here's my take on all the options:
Blaze weapons: close to worthless. They are pretty well rounded when it comes to sheild/armor damage, but the firing pattern is too erratic, and the range is too short.
Neutron weapons: The best if you can fit them in your ship. They weigh a heck of a lot more, but they do great vs. armor, have excellent range and accuracy, and they do OK vs sheilds. Once again, though, this is only if you have the mass to get them. And think twice before using them instead of secondary weapons...
Phase weapons: Very good vs. sheilds, suck vs armor. Range and accuracy are quite good, though, so these are actually what I use most of the time (since I'm not in Voinian space anymore).
Emalgha cannons: God I hate these. They're so slow and short ranged that they totally destroy your maneuverability. In order to accomidate these things, you have to fly right up to the ship you want to hit, and just sit there firing at it. What's more, they take up the same space as Neutron turrets, so I always use Neutron turrets instead, cause they have better range.
So basically, I like weapons which give you more flexibility. The phase weapons are the best for this, due to their speed, rate of fire, range and accuracy, which all allow you to run around in circles and still land shots.
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Everything is catching, yes, everything is catching on fire.