Well, let me cover myself as usual with an, "I'm not a DR" but...
It could be that your kneecap is a little off track, or "runner's knee", or chrondomalacia, or something close to that spelling, all the same thing. This can be caused by several things, for me it was an imbalance in the leg muscles mainly, which can be improved by strength training the legs. Also, the usual advice, make sure you have good shoes. Use the %10 rule when adding time or distance. it could be your feet, the surface you run on, or if you're running a lot of hills, and a number of other things I can't think of.
Sometimes my knee is like that also, just a little sore and warms up after a few minutes and then is fine. Over time though if not taken care of it will probably get worse.
A couple other thoughts. I often got a "cramp" in my left calf/shin. I believe this was because I was overcompensating for my weak right knee. This could be your problem, but if you have it in both knees, I have no idea.
Also, when going through physical therapy I talked with them about the popping, because some days it was worse, better, sometimes it hurt, sometimes it didn't. Bottom line is if the popping doesn't hurt, don't worry about it. That's what I was told anyway.
My best advice is to go to runnersworld.com or another runners source and try to figure out what might be causing it.
And get good shoes! Oh, and stretch it out too, daily or more.
Good luck!