I'm not as big a runner as some people on the board but I like to run 3-4 miles as a cardio whenever I get the chance.
To my knowledge there are two basic solutions to the knee pain issue. Not that it's a huge issue for people who run sane amounts (i.e. not 30+ miles a week every week).
1) Good running shoes have cushion which protects your joints.
2) Avoid heel strikes, if you run entirely on the ball of your foot and never let your heels touch the ground your body will naturally absorb the impact the way it is supposed to naturally. If you're used to running with a "normal" (not natural) gate this is very hard and difficult because it works your calves a lot more.
Also Kyriakos: Some sort of medium-high inensity cardio is absolutely vital for good health. Though it doesn't have to be running, walking most certainly is not sufficient.