The only thing that keeps habitable planets from being totally screwed in space warfare is the fact that they're so damn valuable. I mean, they're in a prtty hefty gravity well, so any defenders on the surface will have to expend energy to get their lasers/projectiles/what have you out into space, while the aggressors pretty much have only to drop large rocks. I expect wepaons designed to destroy or damage planetary populations will be much as nuclear weapons are now, well, I guess that's what nuclear weapons ARE right now.
Anyway, the only truly limited resource is dominance over other peoples, as we expand into space we'll have ridiculous quantities of energy at our disposal, and plenty of other resources. So the battles would be to destroy other nations' spacefaring capabilities and cut off resources. Spacecraft manufacturing facilites would almost have to be in space for reasons mentioned above- i.e. dragging a ship out of a planet's gravity well would be a big waste of energy. And would probably be in defensible locations: asteroid belts (which would also be near resources), orbiting moons, in the debris ring around planets, etc.
Any ship inhabited by humans could not be very maneuverable, since more than a few g's would be fatal, which isn't very much in space really. So fighters would probably be out unless they used sophisticated AI, as even remote controlled ones could simply be jammed. So warships are going to be fairly large. Another advantage of size is that the surface area increase less than the volume when you scale something up, so a bigger ship could have more armor or defenses. I expect armor would mainly be for protecting the crew from radiation, and radiation based weaponry. The disadvantages of size are, well, size, which really isn't that big a deal, since a quadrupling of aspect ratio means you have 8 times the ship, and the fact that engine damage could more easily inhibit maneuverability, since there would be greater sheer stress since the strength of the ships hull would be proportional to the cross section of the supports, whereas the mass to be moved would be proportional to the mass, which increases at a rate of r^3 instead of r^2.
In battle, smaller ships would most likely have to serve a stealth role.
As for weapony, even lasers will take time to hit in interstellar distances, so at longer ranges, a ship that knows it's being fired on can dodge simply by moving erratically. However, it must be noted that the location the beam is firing at can change faster than the speed of light, since it is not an actual physical object and can convey no information from one firing location to the next, meaning that a sweep could be made to hit all probable locations the ship could dodge to. Furthermore, lasers require mirrors in order to operate, so anyone capable of firing a laser will be able to reflect it. This could be alleviated by having arrays of the most powerful lasers possible, but this would be a heavy weapon, most definately. The other disadvantage of lasers, is that they're energy weapons, and so have a significant wave function, causing defocusing over long ranges. Their main advantage is that they cannot be detected before they hit, however, it may well be detectable whether the weapon is powered up before it fires.
Particle beams would not have this defocusing problem, and could be fired at near c, making them almost as undetectable as lasers, but as I said before, the powering up of the weapon system may be detectable.
Unguided projectiles would have to use stealth of some sort. Which in space is pretty easy if you cover it in radar absorbent black paint. They would require some sort of active defense more complex than a simple magnetic field, perhaps something like the active defense system currently being developed which some referred to earlier, which essentially tears the projectile apart with an electromagnetic pulse the moment it contacts the armor, reducing its ability to penetrate.
Guided projectiles would probably see heavy use, as they are the only weapons that can have any sort of accuracy at stellar distances, since they don't have the relativistic time delay when aiming. The best way would probably be to set them up as stealth unguided projectiles set to activate and hit the nearest target after a certain flight time, since once they fired any sort of manuevering thruster, they'd be detected.
Chemical explosives would be far underpowered, so any explosivs would have to be fission, fusion, or even antimatter. They would work quite well as some sort of fragmentation bomb, as there is no air in space to slow the fragments, so they'd probably be made for shredding smaller objects - missiles, stealth fighters, that you only know the general area of.
Battles themselves would probably take place in interplanetary space, since the moment an enemy fleet gets in weapons range of a stationary target, it doesn't have long to live, and ships could be detected long before they arrived anywhere useful. Stealth ships could be a problem, as anything powered down, with light/radar absorbent coating is nigh undetectable. Anything important would probably have satellite grids out at significant range, peroidically sending enerrgy pulses back towards detector stations so to show any object moving throught that space in silhoutte. Warfare would probably be conducted by guided weapons at very long ranges, and any ships trying to move anywhere without gettign hit would have to be flying in rather erratic flight paths, so as to avoid them.