The general principle I've heard many times is that one should not care about noise alone. (That said, noise can help in diagnosis of other problems -- many issues have specific angles of flexion at which noise/crepitus might occur.)
Also, there is at least one completely benign reason for joint noise (I'm not sure how common it is in knees): cavitation creating and collapsing bubbles. This is why you can crack your knuckles.
@robryk thanks for your response, really. For a sliver more context, several of my bones make sounds but the knees are the ones that worry me because I have a separate knee health problem, which I'm not going to explain except to say I'm working with doctors about it and it's successfully managed.