I sometimes have knee problems but as long as I do this exercise, it seems to keep my knee from hurting when I am running. I showed a marathon runner it, several years later we meet up again and told me that he was still running and believes it is due to the exercise I showed him. I am no marathon runner but I do put in about 20 miles a week.

The Excercise: do leg extensions at the gym but instead of holding your feet out straight turn them so that your heels are touching and toes pointed outward (looks like a penguin). You only need to use 10lbs and bend knees at a 45degree angle. You won't feel like it is working but it does! I do this twice a week.

The other thing, if you run a lot, rotate out your shoes every day. This gives them time to dry from sweat and keeps the cusion lasting longer. Hopes this helps!

You have gotten some good advice on the knee pain.  I hope that it helps.  I also want to commend you for asking the right question.  What CAUSED the pain.  Those who don't study history are bound to repeat it. 

The two most likely culprits are overtraining, and shoes.  If you do not have properly fitted shoes, fitted by a running specialist at your local running store, you will want to do that. 

In regards to your training. . . SLOW DOWN (oops, was I shouting?? )  The rest days in the c25K program are for your benefit.  It takes a while for your legs (and knees) to get used to the pounding of the pavement.  Make sure you take 1 day in between running days.  Now, just because we call it a rest day doesn't mean you do no excersize.  If you want to WALK (not run, walk) bike, swim, weight train, yoga, pillades, whatever, do that. Cross training is GREAT for runners (note to self: remember that the next time you don't feel like going to the gym.).  I strengthens your muscles that support your skeletal system and helps recover from the run.  But make sure you are taking that 1 day off from running in between running days.  VERY important.