For me, my knees popping was a sign that my knees were getting damaged. After dealing with this for YEARS and having increasing pain I finally went to an orthopedic surgeon who diagnosed me with patellar femural syndrome (where the knees don't track right in the groove on the femur). I had surgery and it made a huge difference but I still crack from time to time.
Do you have any pain from the cracking or is it more annoying? Do you find that it happens at a certain time of day (like upon waking or after being seated for an extended time) or is it all the time? Do you find that it happens more in warm, humid weather than in cooler, drier weather (my knees are better at assessing the barometric pressure than any weather person :7 )? Have you changed anything in your workout routine or are you wearing different shoes? As you can see there could be many explanations for it and most of them are completely benign.
I would suggest tracking your knees and the popping. Also, make sure that you are getting plenty of water, especially with summer here, as it will help maintain the proper sunovial fluid levels in your joints. Finally, you may want to consider taking glucosamine/chondroitin supplements (I have been taking these for about 3 years now and swear by them). If it becomes worse, becomes painful, or starts to hamper mobility I would recommend getting it check out by an orthopedist.
Good luck to you!
Sabine