I have a horrible back and have back pain for 10 years now (pretty much since I was 18). A few years ago I found out that I have a mild case of Spina Bifida, which has only made me more aware of the back issues. On long rides or if I haven't been on the bike my back does start to hurt and can lead to days of pain.

1. No matter what your set-up is make sure you have numerous comfortable hand positions. I use horns right now and have about three good had positions that slightly change the angle of my back.

2. On long rides, make sure you do go upright every once in a while as to stretch out your back. This will make a huge difference during the ride.

3. Small stretches before and after

4. Core exercises, you don't have to do full sit ups. Getting in the right position and holding the pose (think yoga) will get those muscles working really good.
http://www.mayoclinic.com/health/core-strength/SM00047

I do #1,3(great for lower back),8,9, plank (suspended push up), super man (feet, legs, arms, and hands off of the grown).

5. If that is too much seriously do Yoga a few times a week.

6. Get checked out by the doc. It was years before I was diganoised with an ex-ray that I realized one of the reasons for my back pain.

7. Good posture when your off of the bike.

Hope that helps.