things that performed special roles otherwise unavailable, and would be balanced by the fact that you'd only have X slots per planet, and even moreso for mk II and mk III stations (potentially some specials for the jammer station, too).
well most importantly, in my mind, would be a forcefield of comprable strength to a a mk2. Any 'frontline' world has at least a mk2 at it for me, as well as any important worlds.. Lesser forcefields are distributed to near-frontline worlds in order of importance.
If the action of putting a forcefield on a planet could be a command station module (hell, id be willing to pay knowledge for mk3 stations if i could put a mk2 ff on every planet..)
Basically I am talking stuff other than simple turrets. Heavy beam cannons is an idea, but command stations are VERY fragile - a small bomber wave kills them oh so quickly, and at that point, why waste shots on a turret?
perhaps a large grav field (slows stuff in a large radius, as in, very large..), an localized attrition field? a repulsor gun (like the the experimental displacer, with shorter displacement range?) an 'engineering field' to repair/build in a small radius?
anyway, those are some of my ideas. :p