There's also an armor selection drop down so that you can see the effects of different armor vs phasers, missiles and what not.
Weapon DPS per size vs shields:

Weapon DPS per size vs reactive armor (second best):

Y axis is weapon DPS per unit of size, X is weapon type and upgrades, while Z is distance from 0-990.
Individual weapon comparisons of the same here: 1 2
About this:
-Weapon DPS is per unit of size, with range 0-990 on the Z-axis
-Just treat this as a baseline. Range is arguably more important than sheer damage in practice.
-This also doesn't take accuracy in to consideration. Beam weapons for example have terrible accuracy at range, while torpedo weapons always hit.
-Range is roughly modeled and gets rounded to the nearest hundred.
-Damage Control components only reduce damage that gets past the reactive rating of armor, and isn't modeled here.
-Modifiers vs armor that railguns, missiles and phasers get are all applied here.
Updated for Legends: