This guide is part of the Advanced Shipbuilding Guide series. Due to its extend, I've split off the weapons part into a separate one.
For general shipbuilding and other parts please consult the main guide.
https://steamproxy.net/sharedfiles/filedetails/?id=1984898256

Most ships will have:

• one or two types of main armaments, consisting of several weapons of a kind
  
• one type of secondary armaments, meaning one or two turrets
  
• Anti-Personnel Auto Turrets (APATs)
  
• possibly a harpoon, if you want to take on rescue contracts

Light ships have one AI gunner, medium and heavy ships get two AI gunners (if you don't have crew; with one crew member you still get one AI gunner). Thus medium and heavy ships should have two standard turrets for them, which serve as secondary armament. More is not worth it, unless you are sure you'll always have sufficient crew members to man them.

For the main part of your armament, you have three choices:

• Auto turrets which are controlled by the AI, but can only target engines, deployables and crew. They are the easiest choice, since they fire without player intervention, however they generally tend to be weaker than the other two options.
  
• Fixed weapons, which are fired from the steering wheel. They cause more damage than auto turrets, however they only shoot into one direction, meaning you have to aim them by turning the entire ship. Enemies above or below you are particularly difficult to target, though a tilt module can help to a certain degree (pun intended). Ships with fixed weapons should be highly manoeuvrable, since it would otherwise be easy to get into their blind spot. Thus they are not recommended for heavy ships.
  
• Adjustable weapons, which are also controlled manually and can be operated from either a gunner steering wheel or a control station. They are recommended for heavy vessels, since they can be aimed without turning the entire ship.

Blast Cannons, Gatlings Guns and the Antique Cannon are categorised as adjustable weapons since they can be turned slightly. Unlike other adjustables they can't rotate 360° though and should only be used on manoeuvrable ships.

Since patch 1.17.9 (24 April 2020):

Originally posted by Bronze Johnson:

• Captain aimable weapons are more accurate on lighter ships and less accurate on heavier ships. A spread multiplier scales linearly from 0 to 2.25 from 3k to 30k of captain aimable firepower. Weapons affected by this change are labeled [with accuracy scaling] in their part description.

This means you shouldn't rely only on weapons affected by accuracy scaling, but instead combine them with auto turrets.

I recommend having some automatic weapons (i.e. either auto turrets or AI controlled turrets) which can shoot at targets below you. (They don't need to be mounted to the bottom of your ship though.) This will come in handy when you sunk an enemy, but have not destroyed all engines or weapons yet, since they can do it for you, saving you a dive to the ocean floor.

The first five of the following weapons are available as either manned or auto turrets:

Originally posted by Mech_Hunter:

• Volley weapons are low-velocity (their shells arc) meaning they have a low range and fairly low damage but make up for that with their high are of effect. This makes them very good at destroying armour.
  
• Needle weapons are like the twins but with a faster rate of fire and higher accuracy, they however do less damage.
  
• Breach guns have a high accuracy and damage output while maintaining range and can also penetrate armour for a small distance, they however have small ammunition clips meaning they have to reload often.
  
• Gatlings have the lowest range and are weak against armour but are very effecting at destroying the "softer" parts of a ship (balloons, etc) if used well.
  
• Barrage weapons have good range, good rate of fire, and great damage output but are very inaccurate and need distance for the projectiles to arm.
  
• Precise weaponry (longnecks) have great range, accuracy and having the benefit of not having to reload but they do less damage the closer the range.

Longnecks are only available as manned turrets, they (along with Needles) are my preferred choice of secondary armament. Most of my ships carry one or two of them to make use of AI gunners, also to fight off drones.

Guided rocket turrets are not recommended as auto turrets, since they are causing around 25% less damage than the unguided version and the AI's targeting is quite good. For manned turrets you can consider them, but if your aim is not too bad you'd still fare better with the unguided version.

Auto turrets have a firing arc of 40° horizontally.
Single auto turrets have a firing arc of 360° horizontally.
Both have a vertical firing arc of 40°.

For more details regarding turret weapons please have a look at this guide:
https://steamproxy.net/sharedfiles/filedetails/?id=1971546749

The Blast Cannon comes as raised, straight or lowered version. Both it and the Gatling Gun have an adjustable version which I'd recommend.

Flak, Lance and Quad Cannons have a beam mounted variant with 2300 hit points and 250 mass, the other numbers being the same. I don't recommend using this variant.

Not listed: Harpoons, Magnetic Mine Bay and Fireworks Cannons.

AI ships get an extra 30 m range

Most weapon projectiles travel at very high speeds (from 240 to 1000 m/s) and will reach their maximum range within around a second or less. The exceptions are the heavy cannon (150 m/s), torpedo (110 m/s), antique cannon (75 m/s), barrages (50 to 80 m/s), volley (50 m/s) and missile (40 m/s).

When choosing your main armament, it's recommend to either go for one type or make sure your weapons work well together. E.g. when combining short-range gatlings with long-range cannons, you will not be able to benefit properly from both.
Light ships often field some auto turrets, whereas most medium and heavy ships come with adjustable weapons. The four big cannons (flak, quad, lance and bone) all have the same requirements, thus you can easily swap them for one another if you change your mind.

Recommended weapons
I have found the following weapons to be particularly useful as main armament, other players might have differing preferences though:

• Quad Cannon: A classic preferred choice for many ship designs, relatively easy to handle and long range (400 m)
  
• Rocket Pods (unguided): One of the newest weapons, it has better punch then the quads but less range (275 m).
  
• Battery Cannons: Damage-wise they are average, however especially the heavy and ultra heavy variant allow you to concentrate your firepower very well. Medium range (275 m).
  
• Magnetic Beam Cannon: More difficult to handle than the choices above, since they are not adjustable. In the hands of a capable captain they are devastating, particularly to armoured ships since they pierce through any armour. Long range (400 m).

Adjustable weapon layout
If you opt for rotating weapons, consider where to place them to maximise your usable firepower. There are five common arrangements:

• Front gunner: All guns face forward, limited traverse to the sides though
  
• Central broadside: Guns on or near the centre line, allowing you to shoot to both sides, but not directly forward or aft
  
• Asymmetric broadside: All guns placed on one side of the ship
  
• Superfiring front gunner: Guns are stacked and can shoot to the front and sides. Only works with smaller ships or if you are using the (Ultra) Heavy Battery Cannon or one of the Rocket Pods.
  
• Front and aft superfiring: Similarly to above, also on the back side. Works for heavy ships too, requires a crew mate at a control station for the aft guns though.

Firepower
Each weapon has a firepower listed and the sum of all of them may not exceed your mass, neither during building nor at any time in game. It's recommended to make good use of this firepower budget. You don't have to go to 100% though, since that means that when you lose mass your weapons quickly get disabled.

Hardpoints
All ship weapons provide extra hit points to all connected parts equal to one third of the weapon's hit points. The maximum is 2,000 hp after addition. Thus, balloons and engines do not benefit from this, but hull does.

APAT
To defend your ship against boarders it's recommended to install Anti-Personnel Auto Turrets (APAT). Their range is very limited (10 m), thus place them to secure the steering wheels and crew compartments. On small ships one might provide enough coverage, larger ships should have several.

Harpoons
You will need one harpoon if you want to complete rescue contracts. You can use them for capture as well, however if your ship is fast enough they are not required. E.g. the Blockade Runner relies merely on its speed to complete capture contracts.

Rams
Rams are of limited use and serve as tertiary weapons at best. However, since they don't cost any firepower and don't weigh too much, you can also consider mounting some on nimble ships, usually at the side and the very front of the ship. The higher your mass and the faster your ship the more damage you deal to a rammed ship.