I tend to go for two things when outfitting a ship with weapons:
1. Damage per turn (which means DUC, MB and APB's at the appropriate tech level)
2. Damage per kT.
Note, I can pick one over the other. Right now I am using Quantum Torpedo Vs supported by Meson BLaster VIs and doing some serious damage. The torpedo has a lower rate of fire, but it can do 30damage/kT more than the Meson bLaster in one hit. Since that 30kT of damage can be things like weapons, I have a chance of destroying a ship's weapons before it can fire at one of my ships.
Basically, I call it the "It dies NOW" philosophy.
(I do tend to keep a few pure DUC/MB/APB designs, but there's nothing like a few sledgehammers here and there. Now, to try to mod the Incinerator Beam/WMGs so they are actually nasty for their size.)