I relise this is v0.4 stuff, but here are some early suggestions anyway.
What i mean by ship modules are weapons (beam, missile, and possibly fighters (i'd suggest weapons be discussed in another purpose made thread)), but also "specialist" modules (i.e. subspace teleporter in MOO1 & 2, blackhole generator (moo1)).
MOO3 doesn't actually have many of these things (and i realise that each specialist module will need to be coded individually (because their effects would each be different)).
So here's my list of some 'special modules' that could be considered.
subspace teleporter - transport ships around the combat zone (ala MOO1 & 2).
subspace interdictor - stops above special from functionaling (MOO1).
Beam Focusing device - increases range of beam weapons (MOO1)
Rapid Fire Rack - Increase rate at which missiles on the ship fire (assuming each missile type has a different reload time).
Scanners, Cloaks (self explanatory, and probably discussed elsewhere in these forums).
Engine Booster - Increases combat speed beyond normal combat specs.
Command & Control - Increases efficiency of fighters in the fleet (if fighters are in the game anyway

That'll do for a starting list. Anyone else got any?