The Klein study of the 60s, which demonized the squat as a knee-wrecker, is, of course, a classic - if for no reason other than it is wholeheartedly bashed by every squat lover in the world. BUT, as with any good piece of research, it eventually led people to refute it with time and experience in the gym and further (and hopefully better) research. I could not an online copy of Dr. Karl Klein's research - if anyone has a link, please share it with us.
Although I'm sure there are interesting pieces here and there, I gave up trying to follow the latest trends in S&C research long ago - there are just too many variables to account for in most training studies and usually the conclusions and suggested implications leave you saying either "Well, duh!" or wanting to bash your head against a brick wall. Brad Shoenfeld's piece was mentioned in comments yesterday, so I decided to include it here with a couple of others.
The Biomechanics of Squat Depth by Brad Shoenfeld
How are Partial and Full Squats Different? by Chris Beardsley
Effect of Knee Position on Hip and Knee Torques During The Barbell Squat by Andrew Fry, J. Chadwick Smith, and Brian Schilling