Contrary to what many people think, warmup and stretching aren't the same thing. Before stretching, it is extremely important to warm up. Stretching a cold muscle could lead to injuries, including tears. Five to ten minutes of a light cardio exercise can help warm up the muscles and get your body ready for the workout. A warm up is thought to improve the body's range of motion and prevent soreness. Warming up means loosening the muscles and raising the body temperature and heart rate gradually to prepare the body for exercise.
How you stretch is also very important. The effective and safest stretches are gentle and static, that is performed without any straining or bouncing. The idea is to get into a position where you can feel the stretch but no pain. It consists of slowly moving in to your extreme range of motion and upon reaching the desired tension and holding it for a certain amount of time. Relax, and repeat the stretch if needed. It is important to avoid any jerky movements which could lead to injuries.
Rather than following a long routine of stretching exercises to be performed daily, it is much more efficient to go with a moderate program of stretches to be done on alternate days. Such a program has the best chance to be maintained, something essential for success. Stretching after your work out (especially if a weight training workout) is also supposed to be of great utility. Stretching after workouts helps to reduce soreness from the workout.
An additional component in flexibility and gaining better control of your body, is learning muscle control. The ancient Indian technique of Yoga is as much an art as exercise, and can be of great utility to some people.