Okay, Iztok, there's a flaw in your enhanced analysis: it only considers Huge Hulls. Even when concerning first-second generation weapons that will probably never be used on Huge Hulls. Also, on the research graph, Psyonic Beam appears to be spiking off Plasma, and not Phasors, while Psyonic Shredder is spiking off Graviton Driver 3, not Graviton Driver 4.
Combining info from Iztok's research chart, the wiki, and the game, I've compiled these tables of weapon efficiencies, categorized by tech level in Research Points. The higher the efficiency number, the better the weapons. This contains all hull sizes. Second-gen weapons are grouped together since they all take about the same amount of research, at least on the chart.
Missiles appear to be superior until the Anti-Matter Torpedo, after which you get diminishing returns up until the Positronic Torpedo 2 arrives. Beams meanwhile, begin accelerated progress around high-end Phasor techs and come up with the Doom Ray amazingly early, trumping all contemporaries. Of course, when missile and gun users catch up several thousand TP later, beam users are stuck with an inferior, rather obsolescent weapon.
The absolute best weapon for tiny, small and medium hull sizes is the Black Hole Generator gun. The absolute best weapon for Large and Huge hulls is the Black Hole Eruptor missile.
