Missile launchers: only cruisers were armed with these which made cruisers a bit more useful in battle than battleships (which didn’t have any but did have a ton of armor so as to protect the admiral giving orders). There were many types of missile launchers because there were many types of missiles.
Missiles: the two broad categories of missiles were Nuclear and Conventional missiles. Nuclear missiles would be made big and would be used against big ships like battleships. The nuclear fission explosion would usually be enough to rip apart the armor of those ships. Conventional missiles would be small and made in mass. They had at first light armor and would be very fast, but solid-laser anti-missile guns would be able to quickly shoot them down. Military scientists then wanted the missiles to have heavier armor and energy shields to repel this and the later Delta and Omega classes of missiles did indeed have these. This would make the missiles slow, but the heavier armor would protect them from bullets and the energy shield from solid-lasers. They were still fast enough to avoid shells, big laser guns and fusion cannons. All missiles used the conventional petroleum based rocket fuel.
Ion torpedoes: little is known about these weapons. They replaced bombs for use by bombers in the 23rd century. They were very good at damaging planetary based defenses and starbases.
Ion cannons: these aren’t technically deadly as they just mess up electronic equipment. But since all interstellar ships use computers and electronics to function, these cannons could shut down a ship with just one blast. Then the ship would be a sitting duck for other weapons to target. Deadlier weapons. Planetary defense ships and destroyers are all armed with these but most other ships are not.
Magnetic Confinement Fusion Cannons (or MCFCs) were the ultimate weapons of man as well as Doomsday Missiles in the 24th century. The cannons were very similar to the fusion engines that big ships used (small ships used ion engines). Here is a description of the fusion power of the engine and weapon from the 15th edition of the Encyclopedia Galactica: A major area of study in early fusion power research was the "pinch" concept. Pinch was based on the fact the plasmas are electrically conducting. By running a current through the plasma, a magnetic field would be generated around the plasma. This field would, according to Lenz's law, create an inward directed force that causes the plasma to collapse inward, raising its density. Denser plasmas generate denser magnetic fields, increasing the inward force, leading to a chain reaction. If the conditions are correct, this can lead to the densities and temperatures needed for fusion. The difficulty is getting the current into the plasma; this is solved by inducing the current in the plasma by induction from an external magnet, which also produces the external field against which the internal field acts. In engines, the magnetic confinement process is used to control the reactions and prevent explosions. In cannons, the magnetic confinement process is used to direct the plasma into bolts to be shot out by a fusion reaction. These plasma bolts would be very deadly since there was no defense against them currently.
Defenses
Armor: military ships were defended by armor. The better the armor the better the ships could withstand bullets, shells, lasers and missiles. Heavy armor required more thrust and therefore bigger engines and power sources. The armor is usually susceptible to nuclear blasts and of course is totally shredded apart by plasma bolts.
Energy shields: when ion cannons started being deployed, then ships started adopting magnetic energy shields to deflect the particles. Creating a magnetic field around the ship was required for the shields. This made fusion engines highly popular for ships then because you needed to generate a magnetic field anyway to operate the engines. These energy shields could also deflect lasers very well. Ships had to be very careful when firing ion or laser weapons when equipped with energy shields since firing those weapons when the shields were up caused the particles/bolts to be deflected against the ship and damage it. The commander had to order the energy shields down before he/she ordered the weapons to be fired. Special computers were designed to lower the shields at the precise moment the weapons started to fire. The computers didn’t do that good except in Omega class ships. These shields were totally worthless against plasma bolts, but it remains to be seen whether technology can improve these types of shields so they can repel the deadly bolts.
Energy pulsars: these are neither weapons nor defenses technically, but they are needed to stabilize ships in combat or push away rocks or debris. Space is a vacuum. There is no resistance so when ships fire big guns they get pushed back and risk colliding into other ships. To keep in battle formation energy pulsars are used to combat Newton’s Third Law of motion (for every action there is always opposed an equal reaction). Every single ship in the galaxy has these.