The best medicine for the joints is prevention of degenerative changes, and prevention begins with a proper diet high in complex carbohydrates, relatively low in salt, sugar, fat and protein, combined with sensible exercise to keep the joints strong through use.
There is some debate about the long-term effect of jogging. Many feel that jogging, over a period of years, combines with any inherited weakness of the joints to produce arthritis. The most common joints affected are the knees and the lower back. The intervertebral discs may be most affected by the constant up and down jarring of running. I recommend against running on a regular long-term basis. Save running for the occasional game of basketball, football, tennis, handball, etc.
The best exercise is swimming and the second best is using a machine which works out the arms and shoulders, as well as the legs and heart — such as the Schwinn Aerodyne exercycle. Rowing machines also are excellent, and walking is better than nothing. Whatever you use, it should be used regularly, at least three times per week. This will handle your aerobic needs as well.
Where stretching is concerned, it is important to maintain the normal range of motion of all joints; however, it is possible to overdo it. Vigorous stretching, while it may feel good now, stresses the ligament structures around the joint and causes microscopic tearing of ligaments. Ligaments do not repair themselves. When enough fibers are broken, the adjacent joint will become unstable, and there will be movement in directions for which it was not made. If this happens, there is Prolotherapy, but it is better to avoid the problem in the first place. If you practice stretching, take it easy, do not overdo it.