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I had the exactly same problem when I started riding about a month ago. If it happens in the middle of the ride (as it happened to me), I discovered you can relieve the pain and still manage to get back home if you position the foot on the pedal closer to the heel than the toes. I'm guessing it works as it lowers the minimum angle of the knee. Not sure whether this would be possible if you have clipless pedals though.

Things that you should be careful about:
* Always try to ride at above 70rpm. I'm not sure how much I'm doing, I don't have such an instrument, but in general just try to go in the lowest gear that will let you keep the speed you want to go (without jumping around in the saddle ). Higher cadence is much easier on the knees.
* Stretch before/after each ride, paying special attention to the knees and the muscles around. Do the stretch exercises once a day even when you're not riding.
* Don't start riding too hard. You're not tired and have a lot of energy when you just start, but your muscles and joints are not very ready for full load, so you should go a few km in some low gear to get them warmed up. Even if you stop for a 5 minute rest, don't start too hard, always increase the load gradually.
* Do some strength training on the legs, e.g. climb some short hill as fast as you can from time to time, or go to the gym. This is more of a long-term thing though, you won't see immediate effects.

I wasn't doing any of these things Once I incorporated them in my cycling the knee pain was gone after 2-3 rides. Yesterday I did 205km without any knee pain whatsoever.