A while back, I put up the following two posts about lower back pain and squatting. In the posts, I give some common technical causes of lower back pain when squatting, and how I've successfully dealt with pain and injury in the past.
Squats & Lower Back Pain (Part I)
Squats & Lower Back Pain (Part II)
I want to make it crystal clear that I don't advocate squatting with lower back pain. One thing every trainee should be extremely careful of is pushing into pain. Understand that training through pain is not only potentially injurious, but also creating and/or deepening an association between movement and pain - never, ever a good idea in the long path to movement mastery.