Q:

What measures (and appropriate countermeasures) would be used for sensing and target acquisition in far-future space warfare?

I've never been satisfied with how this has been handled in any sci-fi story I've read, watched, etc. It always seems to get handwaved away with "we have sensor packages of various powers" and "they have stealth capabilities of various effectivenesses". I want to get much more specific than that.
Try to keep this within the realm of basic plausibility and Clarke's Third Law. I want technology in this future warfare to be advanced, but still basically within the realm of what we currently know to be plausible.
This is what I've been able to come up with:

Visual sensing; video collection and analysis comparable to modern day techniques, like what guides the FGM-148 Javelin. In space there's no ambient light, which already presents difficulties with shadows cast by planets, moons, and even other large ships, which would effectively create blind spots unless searchlights were used (which would immediately reveal the craft carrying the light). Add to this that warships will almost certainly be painted matte black, and I don't think visual sensing will be a reliable means at all.
Thermal sensing; works like visual sensing, but with the benefit that spacecraft will emit this naturally (blackbody radiation), so there's no worry about shadows and such. Ships could theoretically defeat this with cooling systems built into their hull plating, but my concern would be that supercooling the hull enough to appear invisible against the black background of space would severely compromise its structural integrity, especially if it includes complex elements like reactive armor. Protruding sensory packages and weapons, and also engines also wouldn't be able to be cooled in this manner without losing all functionality. The best countermeasure I can come up with for thermal sensing would be dispersing a wide cloud of superheated gas around your craft to disguise it (like an IR smoke screen), but I can't imagine this would last long; the cloud would either disperse or cool rapidly, and would need constant renewal to remain effective.
Radar; similar to the current technology. Although we currently have the means to almost completely defeat it (our only current barrier is cost, and this will likely vanish in the future), I'm not certain how the detection could also evolve in the future. In any case, sending out radar signals would probably also allow the detected craft to see the source of the incoming signals, and would compromise the position of the broadcasting craft.

A:

Gravity
Your ships spew out mini nanodrones that just float around in space, broadcasting its' location on an encrypted frequency. 
Since everything distorts spacetime and has gravitational attraction, your nanodrones will naturally be attracted to larger masses. You might get "outlines" of larger ships this way.
When these masses move through your drones, your drones will also be displaced, and as such you can detect the "holes" in the droned areas.
The added bonus for using these nanodrones is that you can program them to identify parts of what it's sticking to, or composition, or w/e. For example, if some happened to be on the Engine, it could broadcast that it detects heat - if some were near missles, it could broadcast that it's detecting radiation from nuclear weapons or whatnot. Perhaps it's actually on a space rock - then it'd just be a slow moving mass of cold rock and report it's speed so that the mothership can confirm if the rock is really a rock (Is it accelerating with no apparent cause? If so, it's probably not a rock...).
Countermeasures:

periodically throw emp waves out to disable the drones in a large area while you travel through that particular sector
antiminidrone drones

Option 2: Use the stars. There are millions of them in the sky. I expect a future civilization capable of space warfare to have some decent star maps. Literally, just look outside the bridge and see which stars are blocked by something. It's probably a ship if it's not supposed to be blocked.

A:

The best two sources on the internet for discussions on Space warfare are the "Atomic Rockets" blog http://www.projectrho.com/public_html/rocket/index.php and "Rocketpunk Manifesto" http://www.rocketpunk-manifesto.com. I might also throw in the Unwanted Blog http://up-ship.com/blog/ for a bit of out of the box thinking.
While you can spend hours parsing the details of various systems and ideas, there are a few fundamentals about space warfare that Hard SF will have to take into account:

There is no stealth in space. Since the background is so cold, any energy emission from the ship will stand out like a bright beacon. Even refrigeration will not help; the refrigeration unit must eject the waste heat. Ships will not only emit thermal radiation, but most practical spacecraft capable of operating in deep space will need nuclear energy (fission or fusion) to power their systems, which means they will also be emitting neutrinos. Even hiding behind a planet won't block neutrino emissions from the spacecrafts power source.
Space is really, really big. So you can see the enemy Stardestroyer from the edge of the solar system? What practical steps can you take? Firing a missile, torpedo or even a Ravening Beam of Death isn't going to help; it will tai anywhere from hours to years for a weapon to cross the Solar System. By that time the target will have moved, the political situation may have changed and any number of systems failures may have disabled the weapon. In a practical universe, most engagements will probably be limited to one light second (just under the distance from the Earth to the Moon) so the targeting systems can acquire the target, take a shot and adjust based on the results.
Practical space combat is going to be very energy intensive. Being able to "jink" your spacecraft will take a massive amount of energy, and the rocket equation will mean carrying fuel for combat manoeuvres requires even more fuel to carry the fuel...space warships will be the size of supertankers. Generating a Ravening Beam of Death (RBOD) might require a linear accelerator a kilometre long to generate an x ray frequency laser that can hit a target a light second away and deposit enough energy to do serious damage at that range. Space warships will be huge, like ballistic missile submarines or aircraft carrier size rather than X-wing fighter sized. Even missiles will become huge ICBM sized devices to accelerate their busses and warheads to as high a speed as possible (the ultimate weapon would be a missile travelling at relativistic speed, which would be essentially impossible to spot, coming right behind it's own light cone, and delivering tens of thousands of Gigatons of energy on impact).
Successful space combat means filling the sky. Filling the sky with sensor drones in a one light second diameter array to get fine grained 3D targeting information. Filling the sky with tens of thousands of coke can sized "Soda Cans of Death" (SCoD) kinetic weapons. Filling the sky with laser energy (the higher frequency the better) to take out the carrier ships with all the kinetic warheads and sensor drones, and the various drones, missile busses and SCoDs as well.

Space warfare will not resemble air or sea combat at all. On the Rocketpunk site, one description of space warfare was a majestic unfolding of a "constellation" of ships and systems, much like a mobile Vauban style fortress. If you use different starting assumptions, you may end up with a different outcome.

A:

Cosmic Rays
Or rather, the absence of cosmic rays. 
A target of any considerable size is likely to be shielded from cosmic radiation. If your targeting system can sense the field of cosmic radiation, and then see a "hole" in that radiation, then you have a potential target. Naturally, you'd probably want some other targeting system in addition to this, to help distinguish friend from foe from asteroid.
Countermeasure
Periodically drop your shielding, or rotate your shielding through different parts of your ship. Or perhaps drop your ship's shielding altogether when battle becomes imminent, and put your crew up in shielded suits, to reduce their footprint.

Note that I am not an astrophysicist and this may all be junk science. I have not done deep research to see if this is plausible, nor do I have the time right now. Please feel free to correct me if this isn't a practical answer.

