Many people with clicking jaw joints often have no pain and and can have clicking joints for decades with no problems. This is why there is much uncertainty and disagreement between practitioners about what to do regarding a clicking jaw joint. Unfortunately there seems to be no long term research due the difficulty of monitoring subjects over 5 to 10 years. the longest studies I have found have only looked at subjects over a maximum of 2 years.
Studies have shown however is that if you have TMJ clicking and pain, this does not get better over time and in fact becomes worse. So as a general rule if you have TMJ clicking with pain it is best not to ignore the pain, even better the focus should be on treating pain and if possible getting rid of the clicking in the jaw joint. Research has shown that subjects with clicking and TMJ pain syndromes show best pain improvement when jaw clicking is eliminated. Further more there is always a risk of a clicking jaw causing a locked jaw as the disc becomes completely out of place, which ultimately leads to arthritic degeneration in the jaw and pain. 
Correcting a click non surgically, which is always the recommend way requires more than physical therapy such as physiotherapy/ osteopathy or chiropractic techniques. This is because the head of the jaw (the condyle) needs to be held in a position that allows the disc to return to its normal position 24 hrs a day. This is done using orthotics or bite plates to hold the jaw in the ideal position, allowing the disc to be “recaptured” and the muscles around the joint to relax.
As a general rule most TMJ clinicians agree that jaw clicking in children should be treated as this is most likely due to a bad bite and correcting the bite with functional orthodontics will stop the clicking and long term degenerative changes. Functional orthodontics which usually involves no removal of teeth and growing the top jaw forwards to allow the bottom jaw to sit further forwards, therefore allowing the head of the jaw to sit on the disc properly. This approach also creates a bigger upper airway as the lower jaw comes forward, therefore reduces risk of sleep apnoea as they grow up.
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2. Sato, S., et al., The natural course of anterior disc displacement without reduction in the temporomandibular joint: Follow-up at 6, 12, and 18 months. Journal of Oral and Maxillofacial Surgery, 1997. 55(3): p. 234-238.
3. Anterior Repositioning Appliance Therapy for TMJ Disorders: Specific Symptoms Relievedand Relationship to Disk Status on MRI. Journal of Craniomandibular Practice APRIL 2005, VOL. 23, NO. 2
4. Emshoff, R., et al., Relationship between temporomandibular joint pain and magnetic resonance imaging findings of internal derangement. Int J Oral Maxillofac Surg, 2001. 30(2): p. 118-22.