Shoulder problems are issues that I see with a lot of people. We tend to lose a lot of our proper range of motion due to all of the sitting and computer work we do. I do like to pick on sitting a lot because it is so frequently a contributor to chronic issues I see in practice. Shoulder exercises, like the ones I am recommending below, are quite often overlooked but should ideally be added to your current fitness program.
I am a huge fan of GymnasticBodies and the work that Coach Sommer does in his Gymnastic Strength Training Course. If you wan more information on shoulder exercises or fitness in general I recommend you check out his site here.

Shoulder Dislocates

Tough sounding name but a great shoulder exercise to promote the health and longevity of your shoulders. Adding this to your daily routine will simultaneously strengthen and stretch your chest, shoulders, and upper back muscles.
It is recommended to use a towel, broomstick or a dowel, so grab what you can and give it a try. Place your towel or dowel rod in front of your hips with your hands in a wide grip, thumbs facing in. Begin raising your arms forward and overhead. Roll your shoulders forward slightly to allow your arms to rotate behind your body. As you bring your arms back behind you, think of squeezing your shoulder blades together.
Start with your hands wider apart and move them closer together as your shoulder mobility improves. The goal here is to aim for a smooth rotation of your shoulders. There should be no pinching or pain during the movement of this shoulder exercise.

Hinge Row

Incorporating the hinge row will help counteract all the forward movement we do throughout our daily lives with our hands out in front of our body. Excellent shoulder exercise for strengthening your upper back and rotator cuff muscles than the hinge row.

Set up a pair of rings so that they are about a foot over your head when you are seated on the ground. Grab the rings and with straight elbows, lift your hips to form a straight line with your body from head to toe. Bend (or pike) at your hips until your torso reaches an upright position so that your arms form a 90° angle at the elbow. Lower down to the starting position and repeat for 5 reps.

Hanging Scapular Shrugs

Performing scapular shrugs while hanging from a pull-up bar is a great way to break up tension in the shoulder blade area. Stiff muscles in the shoulder blade area will cause neck and upper back stiffness. Very common in your everyday desk jocky.

Start out hanging from a pull-up bar with your shoulders in a passive hanging position. Think of allowing your shoulders to hug or squeeze your ears. Leaving your elbows straight, pull your shoulder blades down towards your back pockets to activate your lower traps. Lower yourself back down to a passive hanging position to complete your rep. Try a set of 10 and feel your scapula break free of all unwanted tension.