It's been a long time since I was a runner, but just in case this helps:
I was *running all the time*, gearing up for the annual Vancouver Sun Run, when my knee began acting up.
Complained to my GP (regular family doctor) and she sent me to an orthopedic surgeon AND a "sports medicine specialist". The orthopedic surgeon wanted to operate. I got to the sports medicine guy (same hospital, St. Paul's in Vancouver), and he was convinced that if I just got the right shoes and did the right 'rehab' style exercises, I could avoid surgery.
I went with Sports Medicine Guy's ideas. Turns out I have feet that 'over pronate' and needed to get to a proper running shoe shoe store and have my walk/gait analyzed and a specific type of shoe recommended. After that - it was strengthening my quads. The 'prescription' ? Three sets of thirty squats, three times a day with some big fat weights on my quads (yeeouwwch!). Sounds pretty severe - and yeah, it was kind of tough - but you know what? It worked. No surgery required and my knees don't bother me at all - even though I'm not a runner anymore (pretty much a slug, to be honest).
If my knees start acting up - I know it's the shoes, I need running shoes designed for people that 'over pronate' and I also sometimes need an insert in my shoes to deal with super high arches. Other than that - whenever things go weird, I start up with the squats again - seems to stabilize the knees like nobody's business.
Recommend:
Get yourself to a proper running shoe store - get them to figure out if you have pronation issues and/or arch issues, and get their recommendations on shoes. I know, running shoe stores have shoes that are way expensive, but it's totally worth it - because they do seem to know what they're doing. Getting the right shoes might totally solve the problem. Worth the premium price to go to a proper running store, imo.
See if you can't get your regular doctor to send you to a sports medicine specialist - I was just this regular out-of-shape person trying to get fit, and I ended up getting sent to some guy who deals with major-league sports teams - someone who really knew what he was doing. Saved me from surgery, and gave me tools to fix the problem myself.
Agree with Janet's idea to see a physiotherapist. I was lucky in that my doctor took it upon herself to send me to another doctor specializing in Sports Medicine (instead of physio). Physio would be the norm, no idea why my GP sent me to a sports medicine doctor - might have been she was already sending me to an orthopedic surgeon at the hospital and sports medicine guy worked there too. <---editing to add: I've had very good luck with physiotherapy as well, and agree 100% with Janet that this might be the way to go about figuring out and fixing your knee issues.
Not sure where you are exactly, but see if you can't find something like this (below link) in your area to help with knee/running problems:
http://www.sportmedbc.com/
You can fix this knee pain and still keep running. Might need new shoes, inserts, a 'progam' to strengthen other areas surround the knee or what have you. Might be as simple as hamstring stretches or the like.
Best wishes for getting this fixed.