Full Squat Benefits...

1 IT IS THE MOST PRIMITIVE MOVEMENT PATTERN KNOWN TO MAN
Our ancestors used to perform many daily functions (i.e. harvesting, gathering, hunting, cooking, eating, etc.) in a full squat position

2. IN CASE ANYONE HASN'T NOTICED

We spend 40 weeks in the fetal position (which is basically a full squat) prior to entering this world - do we come out with bad knees?

3 WE SHOULD STRIVE TO TRAIN IN FULL ROM FOR EACH AND EVERY EXERCISE
The squat is no exception.

4 EVERY EXERCISE PRODUCES STRESS
The body then adapts to this stress.

5 CONTRACTION OF THE QUADRICEPS, HAMSTRINGS, AND GASTROCNEMIUS 
MAINTAINS INTEGRITY IN THE KNEE JOINT 
6 SHEERING AND COMPRESSIVE FORCES DO OCCUR AROUND THE KNEE JOINT
Sheering forces that occur in some open kinetic chain lower body exercises, such as the leg extension); however, the large contact area of the patella with the femoral helps to dissipate compressive forces.

7 THE SQUAT IS CONSIDERED A NATURAL MOVEMENT PATTERN WITH HIGH 
FUNCTIONAL CARRYOVER
It is also a safe exercise if performed correctly.

8 DRAWER TESTS ARE PERFORMED AT AN ANGLE OF 90 DEGREES
So, does it make sense to only go down half way where you are most vulnerable especially when greater loads can be used.

9 THE FULCRUM MOVES
the fulcrum moves to the knee joint in a parallel squat as opposed to the muscle belly of the quadriceps in a full squat.

10 PARTIAL SQUATS PERFORMED ON A REGULAR BASIS WILLDECREASE FLEXIBILITY 
11 THERE IS A LOW INCIDENCE OF LOWER BACK PAIN AND KNEE INJURY IN
ABORIGINAL AND ORIENTAL SOCIETIES 
12 OLYMPIC WEIGHTLIFTERS
Even these weightlifters who practice full squats have quite healthy knees compared to other athletes.

13 RESEARCH THAT INDICATES
Although you may find some research that indicates full squats as potentially harmful to the knees, only one study has ever proved this to be true. However, it was performed on a skeleton - the same results do not hold true with surrounding connective tissue. On the other hand, numerous studies show the benefits of full squats. 
It is okay for your knees to travel beyond the toes (just do not relax the knees in the bottom position). In other words, keep the legs tight and try to stay as upright