Here is a good explanation.
http://en.wikipedia.org/wiki/Cracking_knuckles
My joints crack a lot. If I am sitting at my desk with my knees bent for more than 20 minutes, they will almost always crack when I straighten my leg. Same thing with my ankles, neck, back, etc...
During squatting I will hear some cracking usually during warm up sets, but it usually goes away as I get into the workout. I don't think it's anything to worry about unless you are experiencing any pain.