Note: everything I'm about to say is with respect to a "low bar" squat, as advocated by Rippetoe in Starting Strength, because I am a beginner and that's how I am learning to do it.

As I've been teaching myself to squat with little weight (less than 200 pounds), I have learned that one little problem in form leads to a ton of other little problems that together can create a large problem, which for the squat will more than likely hurt your knees than your lower back. The "butt wink" is a product of lack of flexibility usually, and from what I've read, what it does is it takes the load off your hamstrings at the incorrect time during the movement and puts it on your quads, which causes your knees to move forward (VERY BAD). This is because when you break that back angle, the load has nowhere to go but to the quads, and what the hamstrings will not carry will be put on the quads at that particular point in the squat.

This is how I'd go about fixing it:

If you shove your knees out, you will be able to maintain better form deeper in to the squat. When someone says "shove" in this context, in reality all you are doing is keeping your knees parallel with the leg, which is important because if you do not, the tension will shift from your hamstrings to your quads, and thus to the knees, which will cause your knees to drift forward (away from you), which is how you get hurt squatting.

Also, your stance might not be wide enough. Your heels should be about shoulder width apart and your toes pointed out at approx. a 30 degree angle. Those are general guidelines; you can deviate from them minimally to account for your personal comfort and flexibility.

Another thing that no one has mentioned: if you feel a SORENESS, or a STIFFNESS in your back, that is one thing, but with that in mind if what you feel you would consider PAIN and not one of the aforementioned things, then you may have already injured yourself and you need to re-evaluate what you're doing.

I'll elaborate for a second so you understand the difference I'm trying to point out. Since I have started doing squats and deadlifts, I sometimes develop a sore back after athletic activity or lifting weights. It's because I actually HAVE lower back muscles that can become sore, not because I hurt my back. If what I was feeling was pain, then I'd need to see a doctor.

The squat and deadlift are the two best exercises in the gym, but you need to understand them in extreme detail in order to do them by yourself, without the attention of someone who knows what they're doing. I strongly recommend you buy the book Starting Strength and read through it two-three times, until you understand everything in it. It's one of those things where you not only need to understand what you're doing, but why you're doing it, or you will eventually hurt yourself, and become turned off to these mandatory lifts.