Shoes do make a huge difference, mainly running in shoes that are too old. I know it's time to get a new pair when my knees bug me. My suggestion, if you love the heart pumping and sweating of running, but not the pounding is to try an elliptical machine. Not a cheap $400 one, but gym quality such as Precor
http://www.precor.com/hpr_efx.php, that changes incline in addition to tension. The cardio response is the same or even more intense than running, but because your feet never leave the little pads, there's no impact. If you have knee problems however, this probably will still bug you.