As much as every client is different and will have their own unique training needs, there are some things that just about every client can benefit from. I would count thoracic mobility and scapula stability among those things.
If you spend most of your day in a seated position then it is likely that you have poor thoracic mobility. This results in a slouched posture which in turn prevents the scapula (shoulder blades) from tilting back when you lift your arms. When the scapula is not tilting properly, it reduces the space in the shoulder through which the muscles of the rotator cuff travel and over time cause impingement (this is painful and bad!).
So, if you want to prevent shoulder injury you need to ensure that the thoracic spine has adequate range of motion and the muscles that control the shoulder blades, such as the serratus anterior and lower trapezius, are strong enough to move the scapula into the correct position.
Long story short; good thoracic mobility plus good scapula stability equals healthy, pain free shoulders.
Check out the video for a sample upper body warm up which focuses on the spine and scapula. Do this each exercise for about 45 seconds in a circuit fashion before training to start fixing that desk posture.