In reply to Nick Ward:
Ive been in a similar position, buggered my knees in the army basically, Meniscus problems and unfortunately for me I was born with a condition called discoid cartlidge syndrome..One doctor basically said to me that the ball was in my court, if I worked hard to buid my quads up then I may well be able to get to some sort of level of comfort with my knees. I then had an arthoroscopy to trim down my damaged mensicus and wash out all the rubbish that had accumulated around my knee over the years.
At first, I binned the running altogether, stuck to swimming, static bike and exercises such as the leg extension machine in the gym. After the pain sort of going almost completely, I started doing squats and running however I found that the running agravated my knees yet again. I then went and got my gait assessed and having been told that I run like a complete lunatic trying to escape from somewhere I was told that I supinate when I run. I then went off with my new trainers and insoles and I am now running better than ever, I keep up the squats, burpees etc to maintain strength in my quads and I am careful about what running shoes I wear and thus far I have had no major problems, currently in training for the Liverpool Marathon in October and climbing 2-3 times per week.