So, I'm going through looking up weapon/armor stats from a Battle of the Gods game, just because I'm the kind of guy that does that, and found some very weird things... This is from the latest (yesterday's) patch, playing default Terrans, with max tech. For comparison of module sizes, I used Tiny ships (component size increases as hull size increases). I'm also going to ignore the 3 aligned weapon techs (Evil I think) and 4 good-aligned defense techs, because I don't have hard stats for them yet.
So. Missile Weapons. Shortest tree in tech-count (though I presume researching the entire line takes the same time as the other lines). Efficiency in damage per unit of space on the hull takes an early jump due to Stingers doing 2 damage. Don't refit your ships with Positronic Torpedo I, they're less space efficient than Quantum III, if a little cheaper per point of damage.
Beam Weapons. Phasors IV and VI are both less size-efficient than the previous tech (on tiny hulls at least, might not be the case on Huge where it can be more granular). Subspace Blaster looks like it should fit before the Disruptor line, rather than after it, going by stats. Seriously, it blows. The Subspace Annihilator has no ship or starbase improvement associated with it at all. And to top it off, the Doom Ray is the least efficient of all the final weapon techs.
Mass Drivers are where the fun is though. Quantum Drivers are the only obvious efficiency defecit, and the Black Hole Gun is the best of the final weapon techs. Singularity Driver IV and Graviton Driver I, as well as HD Spike Driver III and IV are both the same size efficiency, but cheaper. There are two really important techs in this line. The first is Mass Drivers III, which has the last 2 versions of Railgun. Yes, two weapon techs. Don't bother with Railgun Mk V, the Mk VI is the same price but smaller. The really interesting one is Singularity Driver IV, which also unlocks the Nano Ripper weapon. It's expensive, but it's as size efficient as HD Spike Driver II, 9 techs later. When everyone else is using weapons with 2 or 3 damage, you can pull out the 8 damage Ripper and laugh. Fun stuff.
On the defense side of things, skip Droid Sentries II and III, they're less space efficient than Droid Sentries I. Heck, II and III are identical on a Tiny hull. Shields are fine in general. Advanced Force Fields are same space as regular ones, but a tad cheaper per point. Duralthene isn't worth it for size, and the techs on either side of it are same space, but the latter is cheaper.
I'm gonna do another run, and see how things look on Huge hulls, and post a followup.