CONDITIONING
In addition to cardiovascular exercises, including running, a good conditioning program should include work on flexibility. It is important to avoid ballistic (bouncing) stretches. An excellent reference is the book "Stretching" by Bob Anderson, available in most book stores. Work out sessions should include proper warm-up (jogging, calisthenics, etc.) to increase blood flow, followed by a good 10-20 minutes of stretching.

The most important word for the conditioning program is gradual. Start easy 3 times a week, then gradually increase the intensity and frequency of work-outs. Each session should also be graduated, i.e. the most intense part of the work-out should be in the middle, with a proper cool-down at the end of the session (an easy way is to reverse the warm-up). We also recommend the conditioning program include exercises for the lower leg, useful for preventing ankle injuries, shin splints, and other common lower extremity problems we often see at the beginning of the season.

STRETCHING FOR IMPROVED PERFORMANCE AND INJURY PREVENTION
The Purpose of Stretching
Improves performance by increasing agility, balance, and flexibility and minimizes the chance of pulling or tearing muscles.

Muscle Components Involved in Stretching
Muscle fibers, Golgi Tendon Organ (GTO) and muscle spindles

Types of Stretching
Ballistic--muscle spindles are repeatedly stretched with jerky, bouncing movements; causes continuous resistance by the muscle to increasing the stretch; GTOs are not induced which does not allow the muscle to relax.
Static--a continuous substantial stretch that lasts anywhere from 6 to 60 seconds; the GTO will begin overriding the impulses from the muscle spindles, allowing the muscle to relax; the muscle lengthens and remains in a stretched position for an extended period of time.
P.N.F.(Proprioceptive Neuromuscular Facilitation)--uses the same neurophysical principles as the two previous stretches but has the advantage of causing a reflex relaxation in the antagonist muscle.

The Purpose of Warm-ups Prior to Stretching
Cold muscles don't stretch very well; stretching a cold muscle can strain and irritate the tissue; increases the blood flow and rate of metabolism in skeletal muscle; increases muscle efficiency during the forthcoming exercise.

Benefits of Stretching
It may well be that stretching and warm-up do more to improve performance than to prevent injury.  A 1994 study showed that hamstring stretching and increased flexibility were effective for improving hamstring muscle performance as measured by peak torque values.
Worrell TW, Smith TL, Winegardner J: Effect of hamstring stretching on hamstring muscle  performance. J Orthop Sports Phys Ther 1994;20(3):154-159.

“When running, a full-length stride as opposed to a slightly restricted one will allow you to travel further for the same amount or even possibly less effort. So not only will stretching reduce the risk of injury, but it can also improve your running speed and give you a more natural running technique!”
Jardine, H. Why Stretch? http://balance.net/library/archive_1999/08_26/why_stretch.htm

Stretching increases your agility and balance. Flexible muscle reacts and contracts faster and with more force. Stretching improves flexibility, improves blood supply to the muscles and bio-mechanical efficiency; helps prevent an injury by minimizing your chances of pulling or tearing muscles and alleviating muscle soreness; improves the interaction between muscle groups and improves posture.

Rules for a Good Stretch
Only stretch when the muscles are warm.
Breathe slowly, deeply.
Concentrate on relaxing the area being stretched.
Do not go past the discomfort range; stretching should not cause pain.
Do not bounce!
Stretch before and after exercise.
--- Hold pre-exercise stretches 15-30 seconds
---Hold post-exercise stretches 30-40 seconds
Be sport-specific.
---Different sports use different muscle groups. Concentrate on the range of motions and the muscle groups that are used in the sport.