Running is weight bearing and involves high compressive forces many times your body weight. The eccentric (lengthening) muscle contractions involved with running are also very hard on your body, and the breakdown associated with them requires longer recovery. If you are a large or heavy set person; even more so. If you plan on running long term these are some basic guidelines to follow.

1. Take at least 1-2 rest or active recovery days per week. This means no impact giving your joints a rest from the pounding forces that running produces. Older runners may need 2-3 non-impact days per week.  Cycling, swimming, or other non-impact activities can be substituted.
2. Perform no more than 1-2 "break through" or high intensity interval work outs per week. Speed work puts considerably more stress and the body, and requires more recovery time. This type of training must performed prescriptively and carefully. Try to schedule these key work outs directly proceeding a rest or recovery day.
3. Train in 2-3 day cycles, with a rest or recovery work out in between cycles giving your body to some space to recover from and adapt to the training load. Some athletes will need more rest and less training, especially as intensity increases.
4. Rotate your shoes frequently. A good rule of thumb is a minimum of 3x per year for a high volume runner. You may want to write the date you purchased your shoes in permanent ink on your shoes for reference. Buying shoes is expensive, but so is your insurance deductible.
5. Take the supplements Chrondroitin Sulfate and Glucosamine. I don't recommend a lot of supplements, but this combination has shown efficacy in clinical studies, and in control groups of people suffering from knee pain. One works as an anti-inflammatory; the other helps regenerate cartilage. I know of several orthopedic surgeons who are recommending the supplement to their patients and it may be worth a try.
6. Increase your volume of endurance training by less than 8-10% per week. Bringing your mileage up too quickly is a sure fire way to promote injury. Your body sustains stress (training) and is initially weaker from it, then compensates and adapts to get stronger. If you put too much stress on your body, it can't compensate and continues to break down.
7. Listen to your body. In my experience your body gives you an indication that you are about to sustain an overuse injury. This may be in the form of a slight or nagging pain. If you stop training at that point, you will more than likely regenerate after a few days rest. If you try to push through the pain you may end up with a more serious injury that can take weeks or months to heal.  
8. Periodize your training. Periodization simply means administering the right training at the right time. You prioritize your training into specific cycles that move towards a goal (race). Your training moves from the general to the specific and from low intensity to higher intensity as you approach your peak. The implication is that you are performing your most race like training just prior to your goal race. This means less stress on the body throughout the year because you are not performing high intensity training all season long. An experience running coach can help you set up an annual training plan delineating your training cycles.
9. Perform strength and flexibility exercises to keep your knees strong. One of the more common overuse injuries is "runner's knee." This overuse injury is caused by the patella not tracking properly, much like a tire that is out of alignment. By keeping your quadriceps flexible and strong, particularly your vastus medialis, you can help prevent this condition. If you are an endurance runner you do not need to overwork these muscles or use a lot of weight, but light strength work performed correctly can help prevent injury.
10. Cross train. One of the benefits that multi-sport athletes have over runners is that they are able to perform swim and cycling work outs in between run work outs. This helps reduce the stress caused by the pounding of running, but the athlete still receives the aerobic benefit of training. A good time to cross train is when you have a less specific recovery work out scheduled or a lower intensity base work out. If you use a heart rate monitor you can stay in the same heart rate zone as your prescribed run work out. Swimming, cycling, stepper, elliptical trainer, or even hiking are all good examples of cross training work outs.

An eleventh I would add is to run properly. Unfortunately this is not a quick fix. If you are over-striding or running with a very low stride count your impact forces increase dramatically. By addressing your form you will put less stress on your body. Video analysis is a great way to identify and work on your form limiters.

Matt Russ is a professional coach with over two decades of experience working with athletes up to the professional level. His athletes have achieved numerous regional, national, and international titles under his direction. Matt has achieved the highest level of licensing by both USA Triathlon and USA Cycling, and is a licensed USA Track and Field Coach. His accomplishments include being named "Team USA" Coach by USA Triathlon. Matt is Head Coach and owner of The Sport Factory, a USA Triathlon Certified Performance Center located in Roswell, Georgia. Visit www.sportfactory.com