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We already have three dimensional warfare both in the air and under the water, so human warfare has already been considering it (that extra dimension) for some time.

Combat wouldn't be based around defending the target of the attack. Such defensive tactics would inevitably be too little, too late. As SandThatWasARock pointed out, the sphere around any point in space has significantly more surface area the further away you get. So, If you had an armada trying to defend a planet, you could create a tighter protective sphere closer to the planet, or a loose one further from the planet. Here is a counter tactic for each:

  1. If the enemy favors a tighter, denser formation, use larger ordnance that will damage the protective sphere and the target simultaneously, since the two are in closer proximity.
  2. If the enemy favors a loose, porous formation, use smaller faster ordnance that can evade detection and wreak havoc solely on the target, bypassing the defenses almost entirely.
Both tactics would only be part of larger tactical schemes, but they illustrate how difficult it would be to fight any traditional battles with traditional weapons.

Fleet versus Fleet battles would be less likely, as a single powerful payload could do a lot of damage and if many such attacks were sent, there would be almost no way to stop it, think thousands of suicide bombers the size of cockroaches only two or three of which would need to succeed for complete destruction. Fleet vs. Fleet would be M.A.D., or close enough.

Defense in general is not so viable an option. The best defense would quickly become an offense, the point to remember is that large enclaves who could develop technology faster would have the greatest advantage, though large enclaves in a future of violent space battle would be highly unlikely as a small enemy could very easily destroy a whole planet, or at least it's life sustaining atmosphere.

Tribal nomadic decentralized fleets would be the most likely lifestyle of survival-minded humans in such a future. Large tribes would cut swaths through galaxies along the lines of the richest resource distribution. Smaller tribes could hide by travelling from one resource-poor system to another, staying away from the larger tribes' potential refueling (of any and all natural resources) sources. They might also be able to follow the larger tribes at a safe distance, living off the scraps. Small tribes might specialize in specific technologies in order to make themselves valuable enough to larger tribes to be carried along.

Such battles would be more often a show of force than the need to implement such force. Large tribes would likely go for a larger weaker response to a threat. Smaller tribes for a smaller stronger response. (The difference between cats and bees, for example. A cat will get a clear distance and hiss at an enemy first, a bee will sting and ask questions later, if it isn't dead.)

What is good for defense is good for offense, stealth would be crucial for both, as well as relatively quick motion. Intelligence is also obviously vital. There would be a natural division of intelligence/sensor drones with mainly defensive capabilities and attack drones with quieter short-range perhaps gravity-based sensors. Large fleets of drones are more likely the combat choice in future space conflict for a number of reasons:

  1. One person can control numerous drones with the aid of sufficient computing power and sufficiently complex programs.
  2. Drones are less massive, cheaper to build and easier to manuever. As Shokwave mentions but doesn't explicitly point out, momentum is still a factor. Momentum and thrust info could give targeting computers a relatively small probable cone(more like an inverse bullet shape) of motion that would describe where the target is most likely to be when the weapons are in striking range. The more massive the object the narrower the cone. For small drones, even the act of firing weapons could be used to change the trajectory making its flight path much less predictable to an enemy.
  3. Drones are cheap, you can field more for less and they need be less successful and sophisticated for similar reasons. Drone warfare is akin to guerilla warfare.
  4. Drones can be too small and fast to shoot, even by other drones. Though doubtless this will result somehow (out of necesity) in technologies that will once again make them targetable.
  5. The lines between drones and intelligent mines blur very quickly. You could develop solar-sail propelled drones that sought out non-friendly ships and simply exploded in close proximity.

Drones and mines would quickly clog the first inhabited systems before humans became entirely nomadic as large self-replenishing intelligent mine-spheres would be perhaps the only way to safeguard planets early on. Dedicated destroyers intent on a planet's demise could still succeed with enough firepower.
Avoidance would be the rule of survival in any space war-influenced future.
Energy/Radiation shields or any other new technologies could change the rules but not fundamentally. As long as the environment is an open one and motion equates to security, there will be less incentive to form city-states and sedentary communities.

Basically, space warfare as well as space life would develop very quickly into some strange mutant hybrid of animal herds/packs, tribal warfare, suicide bombing, and microscopic life. It would look similar to the deep sea, with large schools of vessels and swarms of smaller drones heading every which way. The only way to know a war is taking place is the constant explosions while the various larger schools of nomadic ships flee the scene and innumerous beehives worth of drones swarm in every direction and flicker in smaller explosions.

The best source to look at for full 3d warfare models where attacks come without warning from almost any vector at all is either deep sea life or microscopic mono/multicellular life. From which we learn very simple lessons:

  1. Numbers increase chances of survival. (of the species/clan/pack/school/organism)
  2. Look uninteresting to predators. (necesitates less motion)
  3. Offer a service that the bigger more dangerous ones need. (Lampreys and other symbiotic relationships)
  4. Become so big nothing can fit you in its mouth.
  5. Depredate. It makes you stronger. Plus, you can be lazy most of the time and do it every now and again when you feel like it.
  6. The predator is really a slave to the prey. (It goes where the prey goes, it multiplies if the prey multiplies.)
  7. Use your environment for its resources, pollute it with your waste and move on.
  8. One organism's waste may be another organism's resources. (Works on a stellar level too, think stars.)