Missiles, Energy Beams, Mass Drivers. Fun, but... looking at damage types in Master of Magic or Age of Wonders... perhaps there is room for more?
A couple easy additions would be dual-type "Particle Beams" and "Plasma Torpedoes". When I say easy, I mean easy graphically and in terms of the game engine... the interface, of course, would be problematic since there are already icons for missiles, beams, and guns that fill the available space. However, if a ship was limited to max. 3 types of weapons, it would be OK interface-wise.
Particle beam line: Branches off mass driver line. Medium space, medium cost, very high damage. However, as a beam of particles, it is blocked by both shields AND armor.
Plasma torpedo line: Branches off of missile line. High space, medium cost, extremely high damage. However, it is a guided energy ball, and can be deflected by shields AND interdicted by ECM/chaff/point defense.
A "Typeless" weapon - say, a gravity beam - might be interesting as well at very high tech levels.
Gravity beam line: Branches off of energy beam line. Medium space, high cost, low damage. Ignores all defenses.
Lastly - how about some "advanced" weapon versions, like in MOO2 with the MIRV, ECCM, Gatling, and Armor-Piercing upgrades? It may be to late to add these... but, it may not.
Now for armors. In addition to the three "typed" armors, how about a "Hardened Structure" line that boosts ship HP (and thus essentially increases resistance to all damage types)? Also:
Reactive Armor line: Branches off of armor line. Acts like normal armor, but gives +1 missile defense (bonus increases with tech). The armor explodes on missile proximity, causing a premature (and possibly underpowered) detonation.
FTL Point Defense line: Branches off missile defense tech line. Acts as normal missile defense, but gives +1mass driver defense (bonus increases with tech). The PD is so fast that it can target incoming near-lightspeed mass driver rounds, altering their trajectory.
Just some ideas. I like choices when researching or designing ships... the more, the better!