I haven't had the opportunity to really play and find bugs - particularly since the last couple of versions came out, so I am restricting my comments here to the tech tree - in particular to the titles of the various weapons systems.  It may seem picky, but having names that fit the categories and a progress rationale may help the polish of the game presentation.

Beam weapons - assuming the group can be described as emitters of continuous or pulsed energy (EM or otherwise for the more advanced techs) that will (hopefully) be absorbed by the target.

Lasers can cause a phase change (melting, etc.) or other modification of the material’s physical properties (annealing).  I am assuming that the term “laser” is being used regardless of the actual wavelength/ photon energy used. (ie: maser, graser)

"Plasma" weapons don't really fit here, since plasma is composed of high energy charged particles, which do not possess an intrinsic velocity.

Phasors, (regardless of Star Trek) I am assuming will cause enhanced resonation of the target's atoms/molecules and Disruptors even more so - maybe phasors to molecular bonds and disruptors to atomic bonds? 

As for the Subspace Blaster/Annihilator, are you intending that these weapons are capable against ships going FTL (this is the only place I have seen the term “Subspace”) or that they are maybe "Quantumizers" or "Color Beams" that will rip apart subatomic particles - which would seem to be the next step in the progression?

It would seem to follow that the "Doom Ray" would be able to directly convert matter to energy (a true “Disintegrator”) - a step change since you are going from a set of endothermic reactions to an enthusiastically exothermic reaction. (And not one I recommend being anywhere near the business end of. J  )

Mass Divers - Here I am assuming that the description is:  projectors (or launchers) of non-self propelled masses.  The progress track that I think you are going for here entails launching smaller and smaller masses at higher and higher velocities until you get to maximum velocity and then increase the mass of the projectile.  The launcher would have to be recoilless, particularly when you are dealing with the very large masses in the higher techs.

            Miniball weapons are pretty self-explanatory – think maybe something like a rail gun? (Magnetic fields accelerating the projectile.)

            Mass Drivers would seem to be more of the same – either smaller/same mass with a lot higher velocity (more kinetic energy) or bigger masses same velocity (more momentum).  Option a seems to me to be the more logical of the two, and it would allow for greater effective range.  Since there are multiple steps, it may be a combination a followed by b until the next type of weapon.

            Singularity Driver – When you consider that a singularity is another name for a black hole, I think a tech worthy of the name should be quite a lot deeper in the tree – somewhere after you have gone to the smallest masses at the highest velocities.  This may be where Plasma weapons rightfully belong. (Charged particles – ions to electron/proton beams.)

            Graviton Driver - When you consider that a “graviton” is the quantum or “packet” form of a gravity wave (analogous to a photon and a light wave) and has a rest mass of zero, the tech with this name would probably act like a tractor beam.  If we’re taking the next step, the weapon here may be utilizing an ability to bind and/or accelerate non-charged particles – sort of a “Neutron Gun” at start leading to usage of other, smaller sub-atomic particles. 

            HD Spike Driver – I am assuming this is “High Density”, and utilizes something on the order of the degenerate matter found in neutron stars.  This tech would definitely require a high degree of mastery of gravity manipulation. 

Note/Suggestion: Interspersed through the last three sequences either as the last steps or as side techs in a half-step fashion would possibly be the usage of antimatter forms of the projectiles.  I don’t see mastery of the antimatter tech as necessarily a requirement to go to the next category of normal matter, but use of antimatter would definitely kick the impact of the weapon up a notch.  Mastery of any previous antimatter tech and the same type normal matter tech would need to be a requirement of any subsequent antimatter tech, of course.  The additional knowledge might also make it easier to research the following normal matter tech.

            Neutrino Bullets – Neutrinos are very penetrating.  That means they will go through shields very well with little to no degradation.  Unfortunately, they will also go through the target with little to no degradation.  Not the most desirable property when you are trying to pound something into its constituent quarks.  J There is also still some question as to whether they have any mass at all, so they may not really fit the category.

            BlackHole Gun – Back to the true Singularity Driver.  This tech will, like the Doom Ray, represent a real step change.  Rather than having a projectile that after its impact will pretty much cease to be a hazard (assuming the degenerate matter will decay and the other matter beams will spread out to below effective radii), we now have a stable projectile that will continue to suck in all matter that crosses its event horizon.  (Yes, I do know that small black holes are thought to evaporate, and no, I haven’t done the calcs.) Given the vast difference of mass between even a tiny black hole (assuming a usable diameter of the event horizon – its effective size) and anything it is likely to encounter, any velocity imparted to the singularity is not going to be appreciably diminished by any impacts/encounters. 

Missiles - Here I am assuming that the description is:  self propelled guided masses carrying a payload that may or may not be explosive. 

            Stinger/Harpoon – Ah, what’s in a name J .These are pretty good weapons in today’s world.  Who am I to suggest their namesakes aren’t just as good.  The assumption I make here is that velocity, accuracy, and effectiveness of the payload to penetrate/blow a hole in the target at the macroscopic level is continually improving. Given current technology, these would probably start with nukes and/or high Kinetic – kill philosophies and go from there.

            Photonic/Photon Torpedo – Given the name and level in the tree, the payload is probably an explosive device that converts much more payload to energy and is much more effective in directing the energy/photon stream. This weapon may therefore be better as a proximity fused weapon as opposed to a direct contact weapon.

            AntiMatter Torpedo – Back to direct contact.  While the payload itself may not be explosive per se (antimatter HE? – what a thought), the radiation released as it eats its way through the normal matter of the ship has the added “benefit” of frying any electronics and crew in the vicinity.  Interdicted missiles also may just result in clouds of antimatter in your path.

            Quantum Torpedo – Referring to the comments I made under “Subspace Blaster” above, I’m going to hypothesize that the research leading to controlling and directing the energy to disassociate subatomic particles leads through a series of enthusiastically self-destroying devices (Sound familiar?).  They can come in different varieties or “colors” depending on which type of quark you want to mess with. 

            Positronic Torpedo – The positron is just an anti-electron, so unless you are referring to the guidance system (as in positronic brain [kudos to Asimov]) the name really doesn’t fit.  Since the other weapon trees are now dealing with the manipulation of gravity, having this weapon generate a “gravity lance” [kudos to Bujold] or graviton stream would be fitting.  The effect would be like an instant on/off severe gravity well which would rip apart the matter in the immediate vicinity.  Call it the “Graviton Torpedo” or similar.

            Black Hole Eruptor – Following right along, this would take the next step – actually generating enough of a graviton field for creation of a Black Hole right where it does the most good – in your target’s lap.  Again, this is a step change in weapon functionality – for the discussion, see the BlackHole Gun, above.

Note/Suggestion – Think about having diplomatic consequences for races (particularly Good/Neutral ones) for using the ultimate weapon techs in populated systems. 

Edited to shift topic category