Since it's currently impossible to register to forum I decided to send you a mail, I hope you're checking your inbox and reading mails.
My name is Goran, I'm 20 years old, 74kg bw. So the questions is: when I do squats, and I do them really rock bottom, well below parallel, there is cracking sound in both of my knees. It just happens on deep squats, if I go to parallel or slightly below it doesn't "crack". But I do squats as deep as almost touching my heels with ass. They "crack" on 0 kg, on 50, on 110, 120, doesn't matter.
I've got no pain in knees, no problems at all. But I'd like to hear your opinion: should I stop ass to grass squats and just go to parallel to avoid that cracking sound, or is it safe? Thanks, Goran.
I check my email once a day, and don't reply to 95% of the emails I get, which probably makes me look like a complete douche but I wouldn't get a lot done if I cared about what everyone thought of me. Best is to post your questions on the StrongLifts Fan page. I have not decided yet when I'll reopen registrations to the StrongLifts Community, but you can get on the waiting list here.
The cause of cracking joints is still unclear. To be honest, my whole body has been cracking for years (especially my upper-back and shoulders). One theory is that the pop is gas released from your joints. I quit cracking my knuckles years ago, but there is no evidence that it would cause arthritis (source wikipedia). As you point out, the cracking is painless, so there's nothing to be afraid of.
One thing that seems to diminish the cracking is soft tissue work. Some say the cracking/popping joints is evidence of trigger points causing joint stress. You can eliminate those trigger points yourself with a foam roller. For cracking knees I recommend foam rolling your calves, but also your IT band etc.
Regarding Squats, I assume that your technique is correct (knees out and feet inline with your thighs). Better would be to Squat parallel simply because you can lift more weight and you need less hip/ankle mobility to do them correctly. I am NOT against "Ass-to-Grass" Squats by the way, I do them frequently.