The act of running although natural may be very hard on ones body.  It involves highly compressive forces many times your body weight unlike other sports such as cycling or swimming. The eccentric (lengthening) muscle contractions uniquie to running are also very hard on your body, and the breakdown associated with eccentric loading requires longer for a body to recover from. And if you are a large or heavy set person; even more so.  Every sport has a favorable body type; basketball players tend to be tall, football large, but running, especially distance runners such as marathoners, favors a small body type.  If your goal is to be a long term runner the following are some basic guidelines that may extend your enjoyment.  

1. Take at least 1-2 rest or active recovery days per week; more as you age. Active recovery in this case means no impact.  Giving your joints a rest from the pounding forces that running produces allows recovery and inflamation to abate. Older runners may need 2-3 non-impact days per week.  Cycling, swimming, or other non-impact activities can be substituted and may enhance recovery if peformed at an easy level.  Other recovery modalities such as compression, ice baths, sauna, etc.. are also effective.  
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 subsequently requires more recovery time. This type of training must performed prescriptively and carefully, and can be easy to over-do. Try to schedule these key work outs directly proceeding a rest or recovery day if possible and never put them together.
3. Train in 2-3 day cycles, with a rest or recovery work out inbetween giving your body the space it needs to adapt and recover to the training load. Some athletes will need more rest and less training, especially as intensity increases.  Knowing your body well is perhaps one of the most key aspects to enhancing performace.  "Compulsive" runners that have a hard time taking a day off or giving their body the space it needs tend to wear themselves out or peform flatly.
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 knee surgery.
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 training volume slowly and progressively. A good goal to shoot for is no more than 8-10% per week in 2-3 week blocks. Bringing your mileage up too quickly is a sure fire way to promote injury, and there is no way to fast forward performance. After your body sustains stress (training) it is initially weaker from it.  Performance improves only when it compensates and adapts. If you put too much stress on your body, it can't compensate and continues to break down going in the exact opposite direction you want it to.
7. Listen to your body. In my experience your body gives you indications that you are about to sustain an overuse injury before it actually breaks down. This may be in the form of a consistent, slight or nagging pain. If you stop training at that point and use recovery modalities, you will more than likely recuperate after a few days rest.  But 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 will help prevent injury and even increase flexibility.  It also helps prevent muscle imbalances that occur over time with any repetitive act.
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 learn how to run properly. Running is often dismissed as a "natural" sport but professionals actually spend a lot of time getting their form just right.  If you observie a marathon for instance their is a lot of uniformity in the professionals running style and form, but amateurs run nothing like them.  Addressing your running form is unfortunately not a quick fix but it not only helps you peform better, it may drastically reduce incidence of injury. If you are over-striding or running with a very low stride count your impact forces increase dramatically.  Professional video analysis is a great way to identify and work on your form limiters.