The area surrounding the knee is one of the most often injured among athletes and tactical warriors. A plethora of injury prevention paradigms exist on the topic, but from what I see most strength coaches rarely use research-based protocols in this area. Rather, focus here is way too heavy on exercises like barbell squats and deadlifts.
After conducting thousands of physical fitness tests for the military and examining orthopedic and movement function, I think the problem really lies further down the chain. In my opinion, a good number of knee issues among athletes could be headed-off by focusing more on the ability of the body to not just apply force to the ground, but more importantly absorb force through the feet/ankles. It is here that I have noticed vast, vast deficits in both single-leg strength and stability in the ankle joint among those I tested.
Focusing on exercises such as barbell squats actually probably masks dynamic deficits that aren't well-observed during these movements other than knee valgus (knee driving in) and in these cases addressing areas of neglect can be troublesome and often ineffective.
Personally, I've found much success in using single-leg exercises as primary focus for the lower body especially modalities that challenge the feet/ankles to absorb force and demonstrate stability. Some of my favorites include: TRX Squat Lunge/Single-Squat, Kettlebell Reverse Lunges, RDLS, and Lateral Lunges, Sandball Step-Ups using a box, and plyometric movements that evoke lateral hops to include shifting weight along with the body in motion.
Finally, I've found no better movement analysis then using the TRX Single-Leg Squat exercise and a motion-sensitive mobile app camera device to capture, evaluate, teach and provide feedback regarding the impact of stability in the ankle joint and the affect this has further-up the chain or lack thereof. Don't believe me, give it a try, it's worth a one-minute look. Also, this same movement feeds greatly into the solution as well.