There are several diseases that can affect joints. The more common ones, that most people do know are Arthritis; Rheumatoid (autoimmune response), Gout (Uric acid Buildup), and Osteoarthritis (wearing of the joint with usage and age).
Bursitis is also common, and come as a result of inflammation of the Bursa or the cushioning pass of the joints.
Another autoimmune disease that can attack the joints can include Lupus. Sarcoidosis also has a reputation for joint pain.
Certain infectious disease agents also have a reputation for attacking joints; Mumps, Rubella, Poliomyelitis, Mononucleosis, Lyme Disease are common. Influenza and the Common Cold can also cause some joint pain, but never really affect joints directly.