Missile Ships:
More launchers are better than few (well, who would have guessed
)
Ammo, more ammo, even more ammo!!!
Don´t overdo the armor, but some is nice
Don´t forget firecons/active sensors
None-Missile ships:
prepare for a slugfest --> armor/shields are your friend
speed - you want to be able to close with the enemy - FAST!
Like with missile ships, don´t forget beam firecontrols/active sensors
Defensive ships:
Good armor but don´t overdo it.
A little faster than the regular missile boats (so they can get to their assigned escort position)
Lots and lots of AMMs and PD-turrets
AMM-launchers in groups of 5 per AMM-firecon
Did I mention firecons and active sensors?
Personally, I am a big beliver in the "squadrons fight together" doctrine, so all of my warships mount some PD-turrests to protect the entire fleet.
Each ship carries at least a rudimentary passive sensor suite.
Each squadron has at least one, preferably two or three, fleet scouts with the biggest sensors (active and passive) I can get my hands on.
Other than that, have a look at the "Bureau of Ship Design" Forum