There is a dizzying array of weapons choices in Transcendence, and even more in mods. You have as few as two slots and not more than 7 to equip weapons into so it's important to understand what the various weapons do for you. If you talk to people on IRC you may see terms like base buster or skirmish weapon. People will talk about the merits of repeating versus single shot weapons, omni versus fixed mounts, ammo versus ammoless, and dual, spread, and single configurations. This document is intended to help you understand all that.
There are four types of stations in the game. First are the small stations. These include most of the early enemy bases as well as all turrets except Ares (which are ships). Small stations take damage as ships do and don't require special weaponry. Second are the multihull stations. Most stations are multihull. They take only 1 damage per shot from any weapon without a WMD rating and take full damage only from WMD7 weapons. Third are wrecks. They take damage only from WMD weapons. Fourth are the immutable stations like stargates that cannot be damaged by anything.
To deal with enemy stations, especially those that can shoot back, you want some sort of basebuster. This will be a weapon with high WMD and range that exceeds the explosion size of the target. Preferably you want something that exceeds the weapons range of the target. The most commonly used base busters are howitzers and missiles. In a pinch repeating, high rate of fire, or passthrough weapons can be used against bases because each hit does 1 damage, but they cannot clear wrecks. There is one station type with walls that leave wrecks when destroyed. Unless you slip shots through a narrow gap between the walls this station can only be destroyed with WMD weapons.
Early on bases have low enough hitpoints that you don't need to worry about basebusters and many are small.
Skirmish weapons are weapons for fighting other ships. In my opinion the most important trait for skirmish weapons is rate of fire. The second most important is damage per second. Most weapons can be used as skirmish weapons if enhanced +fast with a weapon optimizer rom. There are short and long range skirmish weapons. The shortest ranged weapons are most suited to faster ships because many enemies will attempt to maintain some seperation.
Tracking or Fragmenting missiles or MAGs, as well as the Strelka missile line are appropriate for use as skirmish weapons. They can do great damage to opponents you would not otherwise be able to handle because they can be fired at the same time as your normal weapon, and fragmenting or tracking missiles are relatively forgiving of sloppy aim.
Omni weapons are in a sense a subset of skirmish weapons, but they aren't selected on the same basis. Omni weapons rarely have decent rates of fire or damage per second competative with fixed mount weapons of the same level. However, because they are turreted and take account of the target's velocity in aiming, Omni weapons are the most forgiving of poor aim. They can be used during defensive maneuvers in a way fixed mount weapons cannot.
The other major benefit of omni weapons is that they are not granular. Fixed mount weapons can only be fired at one of the 40 ship facings. If your target coves e.g. a 3 degree span centered at 13 degrees, you cannot hit it with a non-tracing non-omni weapon.
Because of the granularity of aiming at long range you can't really snipe anything but bases, but you can make long range attacks on targets defending a base. The simplest is what I call “drift sniping”. Generate a small velocity tangential to the target base and fire continuosly at it from long range. You will mostly miss the base because, but spread weaponsfire throughout the area around it where the defending ships patrol. This is most suited to Howitzers and the Katana Starcannon because they are ammoless, but is also viable with non-tracking missiles, particularly heavy fragmenting missiles like Ares Micronukes, the Akan 30, and the Kiloton cannon.
Because of the way resistances are distributed among opponents not all damages are created equal, even beyond the “ladder of damage types” issue. You should allways seek to either have weapons in at least two damage types or have high type weapons.
These are approximately equal. Most differences are not inherant to the damage type. All laser weapons in the default game are beams with a high shot speed. All kinetic weapons except the flensers have a medium shot speed. Apart from the flensers kinetic weapons tend to be short ranged. All lasers have the same range. Outlaw ships tend to resist laser. Pirate ships tend to resist kinetic. Neither resists enough to make either damage type useless against anything, particularly given the shield advantage the player usually has.
Early on particle is king. Any early particle weapon can make the first stage of the game easy in a way that blast weapons usually don't. Nothing common before St. Katherines resists particle, and several ships resist blast. Unfortunately particle goes allmost completely obsolete not long after St. Katherines. A major enemy ship type reflects particle, and several enemies resist it. During the stage when most enemies use particle weapons allmost every enemy resists it so some degree.
Blast is slightly weaker than particle in the early game, but far stronger in the mid game. Late game there are major enemies that resist either and a couple that resist both.
Ion is one of the most versatile damage types. Only four opponents resist ion: The Dwarg Behemoth, the Aurochs mine layer, the Centurion, and the Centurion X. Of these, the mine layer only appears in missions. Ares armor is vulnerable to ion.
Thermo is weaker than ion in that more things resist it and nothing is vulnerable to it, but there are no true base busters in ion.
Higher damage types are pretty much unresisted. Combined with the ladder of damage types this makes positron, plasma, and antimatter weapons devastating. The lone Dark Acid weapon in the current game has such low damage its position on the ladder of damage types is of little benefit, but it will allways do that damage.
Configurations matter mostly for skirmish weapons. Apart from the dual flenser there are no base busters that are not single mounts. Unlike some games all defenses are percentage based so a dual 1d4 weapon does, at the first approximation, exactly as much damage as a single 2d4 weapon of the same damage type. This isn't exactly correct because of roundoff errors. Transcendence allways rounds damage down, meaning the same total damage in fewer shots is better, but the difference can never exceed 1 point for each shot difference.
Most weapons are single mounts. You fire one shot and one shot comes out. Nice and simple.
There's not a lot of difference between these two types. They split your shots into two parallel lines. This gives you the possibility of scoring half damage on a target you miss by only a little bit, but also the possibility of scoring half damage when a single shot would have hit the edge of the target for full damage. They're slightly more forgiving than single mounts especially at close range, but remain useful at long range.
Spread weapons tend to be forgiving, but rarely score full damage. They are generally short ranged. The wider the spread the harder it is to get multiple hits on a target.
Repeating weapons are usually single mount, though some dual repeating weapons exist in the early game. When you fire a repeating weapon it fires multiple shots. You can either fire without turning to have them hit the target in the same place as with a single mount, or you can turn while firing for a spread effect. When turn-firing your spread is allways 9 degrees between shots. Because of an error in the description code repeating weapons fire one shot more than listed.
There are just three particle configuration weapons in default Transcendence. The PK-25 Morningstar and Dvalin Ion9 are wide angle weapons that function like spread weapons. The Plasma Torch is such a narrow angle weapon that it is effectively a single mount weapon.