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Missiles are generally not so great.
It is preferable to have all guns with similar charge time. Ions dont need this, so ions are awesome. For the final battle it is very nice to have a good bomb and massive amount of firepower (lasers/ions).
I don't like beams that much as these need to be supported by other weapons to work. Missiles are terrible except, maybe Swarm one, and even then I would like to have a good bomb instead.
My personal favourites are: Ion Blast I/II, Burst Laser II, Breach Bomb I/II.
The Pegasus Launcher is really awesome. It can get through defense drones if there are, and 2 for 1 missiles with adequate charge time can really take down any system.
A Burst Laser MK3 requires an enormous power expenditure, so while it's nice to have, it demands a huge investment.
If you get the chance to grab a weapon preigniter, defintely get it. It's worth an accessory slot. Getting to drop a bomb on the missile bay before the battle even begins is priceless.
However, I'd like to give a special mention to the Ion Blast and Heavy Laser.
1 power, less than 10 charge, and pretty shiny results. They're also cheap to buy. (Ion Blast is, what, 30 scrap? Not bad for basically an extra laser).
They're not so great if you have lots of weapons, but if you have some really powerful high-power users (like the Vulcan, but that's too rare; a better example would be Breach, Ion Blast II, Halberd Beam) then they work brilliantly alongside those. The HL is really amazing for just squeezing in a whole extra 2 points of damage alongside your barrage.
I would also like to say that Breach Missile + Hacking + Preigniter + A whole bunch of weapons is amazing. Hack helm, throw your Breach at their shields (that'll take 2 shields down instantly), then fire all your remaining stuff (often Flak and BL) at their weapons system.
For added carnage, board the wreckage afterwards as their shields system is on half health and their weapons system should be basically trashed.
Burst Laser II and Flak I are the best in the game, but BL II is rare and Flak I is common as dirt.
The Heavy Ion is garbage. The Chain Ion is little better. The Ion Blast and Ion Blast II are both reasonably good. The Ion Stunner is even better than the Ion Blast I. The Ion Charger is similarly serviceable.
Most missiles suck. Artemis is okay and is the only one that is even mediocre.
Burst Laser I is serviceable. Burst Laser II is phenomenal. Burst Laser III is absolute garbage. Heavy Laser is a very nice 1 power weapon. Chain Laser is goofy but semi-serviceable. The Chain Vulcan is awesome, in the sense of being really fun to see a machine gun laser rip apart everything by itself, but massively overrated and takes forever to spin up. Both Laser Charger weapons are reasonably good.
Pike Beam is a very good early weapon but becomes much less useful later in the game. Glaive Beam is super powerful but a glass cannon, and needs a lot of support and strong defense. Halberd Beam is the best rounded of the beam weapons.
Anti-Bio beam isn't recommended for general purposes, but has some niche uses. Fire Beam similarly isn't an all-purpose weapon but has some VERY strong uses.
As for bombs: Breach Bomb II is fantastic along with boarding (but beware being trapped in rooms when enemy ships have upgraded door systems). Ion Bomb is not as good as it was, but still pretty good. Fire Bomb is really only useful for boarding, specifically with Rock. Otherwise, enemies put out the fire too fast for it to be much use (whereas the Fire Beam can set half the ship on fire in one shot). Healing Burst and Repair Burst are of very limited use, okay if you have nothing else for that one power. Small Bomb is a wonderful little weapon for one power.
You'll very rarely have to worry about Crystal weapons, but if you do, the Heavy Crystal II is complete garbage, and the Heavy Crystal I is awesome.
In general, bombs are better than missiles because although they can be evaded, they ignore defense drones.
You'll end up using nearly everything you acquire at one point or another, but other than the really good weapons, you should try to avoid spending any scrap on them unless you HAVE to (you're unable to kill the ships you're encountering or you're about to be unable to because of moving to the next sector).
tl;dr don't use missiles if you can avoid it. Heavy Ion is garbage. Burst Laser III is garbage. Anti-Bio Beam is (usually) garbage. Fire Bomb is of very little use. Chain Ion is (mostly) garbage, although it is okay in long fights.
Charge II is much better than Charge I. Charge II is pretty decent because a) it can fire one laser shot in 5s by default and 2) on stronger ships, four lasers (in 20s) is not too bad at all. Charge II belongs in the same category of "Good" as Charge Ion IMO.
Meanwhile, Charge I hogs two power for two shots; it's basically as good as BL I, which is "Not very." It's usable but not great.
Breach is also pretty good IF you have a whole bunch of weaponry to take advantage of blowing a hole in their shields system. (Breach + Large quantities of lasers = Good). However, like every other missile in the game it has a habit of missing at the most unfortunate times... Certainly not something you'd buy, but if you get it for free it can usually be accomodated nicely in a loadout.
Both of these have the (minor) advantage that after shields are down, you can put them on autofire and treat them as fast-firing Basic Lasers. But yes, Charge Laser II is (usually) better than I.
(Exception, the 1 power Charge Laser that Stealth C has is pretty good. But I generally didn't mention "special" weapons like that since you can't get them anyway.)
This is another where the big thing is whether you have some way of making sure it hits, like a 1 power hacking system, where you can hack the piloting to ensure it hits. Anything where you can miss is disastrous, and a single Defense Drone I makes this weapon nearly entirely useless.
I just don't like a 4 power hit-or-miss weapon like this. It's not going to be in my final buildout either because just the single DD I on Phase 2 renders it useless.
As for the last point, you're almost always going to use weapons you get for free, even absolutely terrible crap like Heavy Ion (IMO worst weapon in game). I have taken atrocious crap collections to the flagship just because they were free, semi-worked together, and I had better things to spend scrap on.