I can't recommend Michael Boyle's books enough - "Functional Training for Sports", and "New Functional Training for Sports". He trains athletes at a national and olympic level, and injury prevention is a key theme running through everything he says. In contrast to Starting Strength et al, he actually makes the point that heavy bilateral squats and deadlifts are often too hard to teach and do well. He doesn't recommend doing back squats at all. The programs they use for athletes focus on single leg work, the argument being this is both safer and more 'functional' (how often do you back squat heavy stuff in the real world?).