I have cracking knees especially in my left knee and sometimes in the right one too, but not much. I have checked it they said it's nothing but it's uncomfortable. I dont like the feeling when squatting and when I go up, the knee just pops back to its place in the knee cap area. I am afraid it will evolve into something bad. Is there any exercise to strengthen the knees and stop this awful sound?
I had the exact same problem when I started training and I could seriously improve the "cracking" noise and the related feeling over time. I read somewhere that this is caused by uneven distribution of fluids in the joints, but I can't find the source anymore.
What's actually helped me was a lot of different leg related exercices, even those where the knee joints are not directly used. Squats, leg extensions, leg curls, hip abduction and adduction, running, cycling, elliptical trainer, ... From that list I think running and the leg curls had the most effect, especially when using cables instead of machines, but I think the key was the broad spectrum of exercises.
As I said I could improve my situation, but the cracking noise sometimes still comes back, especially if I did a halfhearted warmup.
Since you said you had it checked out:
I hate to say it, but one of the best exercises for your knees is the squat. I'd check out this video with Mark Rippetoe (a respected coach) for good information on proper form to get the most out of it.
By that time your knees, and all the rest of your stabilizing muscles should be at the same level.