Locations of strategic or tactical importance:
-Jump nodes (inter-system mobility)
-Lagrangian points in systems; good places to put installations, shipyards, sensor arrays, communications outposts and other assorted stuff like that at.
-Geocentric orbit altitude around the equators of planets. Also, following speculation assumes that subspace jumps from low gravity potential to high gravity potential (ie. from low orbit to high orbit) require more energy than simply jumps from "deep space" to another location in "deep space" (meaning, reasonably far from any significant gravity sources). Intersystem jumps seem to be a bit different because the nodes seem more like natural phenomenons than the intra-system jump nodes that are (again based on my assumption) temporarily generated by the jump drives of the ships using them.
Hence it would make sense that capital ships would be fairly reluctant to settle on low orbital altitude - getting away from there would require a lot of energy, and while possible, it would also likely mean longer recharge time for the jump drives. And for the practicality of geocentric orbits, it's unlikely anyone would willingly sacrifice such an energy advantage.
Based on these assumptions, it would be very rare to see capital ship combat below geocentric orbital altitude (which depends of course of individual planets' mass and rotational period). Transportation from surface to geocentric orbits could be done either via space elevators, or transport space craft. Escorts of important transports would be most sensible to manage with atmospheric fighter forces based on the planet, and the actual space fighters that we are all so fond of; most likely these fighter squadrons would be based on installations positioned on the geosynchronous orbits.
These installations would be the main port of goods from planets to the capital ships (and other planets of course). Food, water, recruits, munitions, maybe some fuels, spare parts and very likely smaller-than-cruiser sized ships would most likely arrive to your fleet via this route, and any meaningful volumes of this sort of stuff require space elevators - hence geosynchronous orbital isntallations are a necessity. Losing control of these installations would be equal to losing the planet as a source of resources, as you would be cut off from the space elevators and using transport ships would be a logistical nightmare beyond any hope of success as far as I can see.
For a capital ship to go below the geosynch orbital plane there would need to be a pretty good reason for it. Accurate surface bombardment for example would actually be easier from geosynchronous orbit despite the distance (although you would need to take the coriolis-effect into account) than from low orbit where you can only make passes at any given target during fairly limited window of opportunity. Related to this, polar regions would be easiest to defend on a planetary surface and also likely to be the last strongholds against an invasion force.
-Off-planet resources. These would include iron asteroids, comets with significant heavy water concentration, rare elements and other miscellaneous stuff that can be found in the space. The major advantage in these is that they are already in space, so you don't need to haul them there from the planet surface. Which pretty much means if you have a nice huge iron asteroid, you would likely build a shipyard next to it and start making ships out of it rather than ship the iron somewhere else.
Or whatever the ships are made of, although I would still hazard a guess that capital ship frameworks are built of steel/iron. Fighters might have composite, titanium or aluminium hulls, but capital ships most likely have iron frameworks. Or maybe steel concrete, although making concrete in vacuum would likely be... difficult (what with the water doing funny stuff based on nonexistent pressure and very variable temperatures).
So, this sort of resources would likely be on the list of things you would want to keep in order to replenish your fleet.
