You won't be building a PDC if you want to put it in orbit or near a jump point. PDC's are ground based only. What you want is a base, which is simply a ship without engines(and remember to remove the fuel storage unless it is a fuel base).
Missiles tend to be a staple of bases(and PDC's) as you are not going to be able to chase after an enemy to get into beam range. Due to this you may want to design missiles with longer range than you use for your ships, or design a multi stage missile. As you don't have engines taking up space, you can afford to go with significantly larger sensors/fire controls.
Beam bases at jump points however can do very well as they can get there heavy damage strikes off before the enmey can see them due to the jump blindness. Point defence beam bases at colonies can be helpful as your ground based PDC's cant use most beam weaponry due to the atmosphere of the planet. Also remember that if you are mounting beam weapons on a base you will want to put them in turrets unless you feel that your racial tracking speed alone is sufficient.
Small and large bases each have their own benefits and drawbacks, particularly if you compare equal total tonnages. Small bases are far less likely to be taken out by a single lucky hit, particularly missile bases where you can suffer secondry explosions from your magazines. Small bases can be built earlier beofre you have had the chance to expand your shipyards to the size needed for large bases. They are also individually cheaper so you will get some protection out faster than the much longer time it will take before a large base is constructed.
On the other hand large bases have a lower percentage of the total tonnage being used for non weapon systems (crew quarters/damage control/armour/sensors/etc). Also shields tend to end up more effective on a single large base than an equal number of shield generators spread over a number of smaller bases. Similarly armour becomes more effective as it becomes less likely that a hit will strike at the same point as an earlier hit. If you utilize CIWS, that is limited to firing at missiles targeted at the base they are mounted on, so favour single large bases with many CIWS mounted rather than multiple small bases with only one each.
My personal playstyle is to use some small bases initially to get some basic protection then build larger bases as my shipyards become able to do so.
Using terraforming bases rather than ground based terraforming installations is cheaper per unit. One thing to note, each terraforming base will only get the bonus of the officer assigned to it, so it normally works out better to build a few bases with multiple modules, to take advantage of your officers with high bonuses, rather than a large number with only one each(assuming you have the shipyards to support larger bases of course). The terraforming bonus of the governor assigned to a colony only effects installations, not those in orbit, so if you have a couple of governors with very high terraforming bonuses, it may be worth building installations instead as they will all take advantage of his bonus.
