As people have mentioned, while figuring out the angles between the points is relatively easy, determining the way that wind and gravity will affect the shot is more difficult.
Wind and gravity are both accelrating forces, though they act somewhat differently.
Gravity is easier, since it has both a constant direction (down) and magnitude regardless of the object. (Assuming that you're not shooting things with ridiculously high velocities). To calculate how gravity will affect the velocity of your object, just take the time since you last updated the velocity of the object, multiply it by your gravitational factor, and add it to your current velocity vector.
As a simple example, let's think of an object that is moving with a velocity of (3, 4, 7) in the x, y, z directions, with z being parallel with the force of gravity. You decide that your gravity value is -.3 You are ready to calculate the new velocity. When you check, you discover that 10 time units have passed since your last calculation (whatever your time units are...perhaps ticks or something). You take your time units (10), multiply by your gravity (-.3), which gives you -3. You add that to your Z, and your new velocity is (3, 4, 4). That's it. (This has been very simplified, but that should get you started.)
Wind is a bit different, if you want to do it right. If you want to do it a simple and easy way, you can make it like gravity...a constant force in a particular direction. But a more realistic way is to have the force be dependent on your current velocity vector. Put simply: if you're moving exactly with the wind, it shouldn't impart any force onto you. In this case, you simply calculate the magnitude of the force as the difference between its direction and your own.
A simple example of this might be if you were moving at (3, 0, 0), and the wind was moving at (5, 0, 0), and we can give the wind a strength of .5. (You also have to multiply by the time elapsed...for the sake of this example, to keep it simple, we'll leave the time-elapsed factor at 1) You calculate the difference in the vectors and multiply by your time difference (1), and discover that the difference is (2, 0, 0). You then multiply that vector by the wind strength, .5, and you discover that your velocity change is (1, 0, 0). Add that to your previous velocity, and you get (4, 0, 0)...so the wind has sped the object up slightly. If you waited another single time unit, you would have a difference of (1, 0, 0), multiplied by your strength of .5, so your final velocity would then be (4.5, 0, 0). As you can see, the wind provides less force as you become closer to it in velocity.) This is kind of neat, but may be overly complex for game ballistics.