Different games have slightly different physics, but then again, they also have different gun models with different muzzle velocities making the difference between games irrelevant. It's primarily a relation between gravity and muzzle velocity and that works across game titles.
If you just want to get used to being able to get used to judging ballistic trajectories (None of that instant-hit gun mechanics of certain FPSes), i can recommend Sniper Elite. It's an old but easy game to play. You can turn windage on and off. And you'll learn about bullet travel time, limited time to aim when holding your breath and, most importantly, parabolic trajectories.
This is just to get you used to not having an instant-hit weapon. Each game has its own bullet mechanics, so you'll still need to fine tune how you judge distances specifically to it.
http://www.youtube.com/watch?v=v5lkUPOruPcAs a tip for your mouse you have two options when fine aiming:
#1 decrease the mouse sensitivity until it takes you atleast three swipes to turn around. Sucks when you're in CQB but good for fine aiming when sniping long distances.
#2 Press down hard on the mouse and squeeze hard on its base and the mousepad with your fingers. This creates extra resistance on the mouse and lets you move it in tiny increments. Good for when you want to maintain high sensitivity for when you're not sniping. I use the claw grip and hold the mouse with just my pinky and thumb, but then i grip the mouse tighter and downwards when i'm in sniping mode (still holding with just those two fingers), this also drags my skin against the mousepad adding more resistance. When i'm done sniping, i relax my grip and i'm back to being able to do a 180 in 1 inch.