I started road cycling almost 3 years ago because of knee pain. Yes, because of it. My goal was to enhance my fitness and yet save my knees. So I learned to spin faster. A bike computer with cadence or, even better, an HRM with cadence is highly recommended. As I was out of shape spinning faster resulted in quickly getting out of breath so my average RPM was around 60-70 when I started. After a few month I was able to reach 70-80 and now I average about 85-95 which is very comfortable. My knees are now fine without pain except for an occasional bit of tendinitis after some hard climbs.
Learning to spin faster will surely increase your fitness and cardiovacuslar system while saving your knees for when you need to crank it up. Lance Armstrong is the perfect example of the efficiency of higher cadence.
Your knee pains are probably nothing more than tendinitis and due to a lack of training. Start slow and progressively increase your mileage and output.