Squats get a bad rap because people believe that squats can hurt the knees. Of all the exercises a person can do to strengthen and stabilize the knee, a properly performed, full range of motion back squat is the best exercise. The qualifier here is "properly performed". By that, we mean a squat where the top of the thigh is parallel to the floor (parallel depth) or lower than that. Any higher than parallel is what causes knee injuries during squats.
Another common mistake I notice is people turn the squat into a quad exercise. Front squat siguro, but as for the back squat, it is a posterior chain dominant exercise (it should hit your lower back, glutes, hams).
With regards to form, the hips should be the first to break, not the knees. Many people go "down" when they squat. Better is to go "back" (break at the hips), then down. Imagine you are sitting on a toilet bowl.
Other key points:
> maintain lumbar arch
> push knees out
> maintain core bracing
> tight scaps
> tight grip
> chest up
> on the way up, EXPLODE using your posterior chain (contract your glutes as strongly as you can)
If you really want to refine your form on the squat, I suggest you do wall squats (
YouTube - Elitefts.com - The Wall Squat) , and goblet squats.
@slick rick: 5/3/1 is a powerlifter oriented program.