The pec deck, also called the chest fly machine is designed to work your pectoral (chest) muscles. However, it can put your shoulders in an unstable position, causing stress and possible impingement of the shoulder joint. Users often roll their shoulders forward; adding weight to this position leads to damage and pain.
A much better way to work the chest (and your shoulders, triceps and abs) is the pushup. (See post from Feb. 2011 for tips on pushup form: http://wellerbodiespersonaltraining.blogspot.com/2011/02/cheating-pushups.html).
If you feel you must isolate the chest muscles try a dumbbell fly instead. For those who absolutely cannot give up the pec deck go light on the resistance, and try to keep your shoulders from rolling forward.