There is a physical therapist that states that all musculoskeletal pain is caused by imbalances in your muscles. If your sort these imbalances out, no pain.
The way to tell if you are imbalanced is to look for a few things:
When you are standing around, look at your feet. Are they pointing forward? If not there is a problem somewhere.
Also if you stand up straight, there should be a vertical line downwards along your side through your shoulder, elbow, hip, knee and feet. If the line isn't vertical, you have a postural problem somewhere.
The reason these are mentioned is that say if your feet are pointing the wrong way, this would say the hip was out of place, which would mean the spine was out of place which would the shoulder blade was out of place which could lead to neck/shoulder pain. I am sure you get the idea.
The therapist is Pete Egoscue and he has written a book called Pain Free:
http://www.amazon.co.uk/exec/obidos/ASIN/0553379887/qid=1060767002/sr=2-1/ref=sr_2_3_1/202-8353950-5703060
In his book he has chapters for each major section including ankle, knee, hip, back neck etc.
There are stretches/exercises to get rid of pain for that particular area.
I highly recommend the book.
Having said that, most of the exercises in the book come from yoga. So you could find yourself a good yoga teacher, let them know your problem and try out a few yoga sessions and see how that helps.
Another person who does something similar to Pete is a guy called Paul Chek.
http://www.paulchekseminars.com/
He has practitioners in this country, one of whom has written an article for this website. The writer is Jon Bowskill (you can search for his articles using the advanced search facility on the Health page). Here is one I have found:
http://www.runnersworld.co.uk/news/article.asp?SP=&v=4&UAN=488
As I have documented elsewhere on these forums, I had knee pain. Went to physio, diagnosed as patellar mistracking. Couldn't be ar**d to do the exercises. Saw a podiatrist who prescribed orthotics as if they were the solution for every ailment. Knew this was not true.
Started yoga and no more knee pain. Also have the advantage that yoga stretches out the whole body and I feel completely relaxed and blissful at the end of a class.
Sorry for rambling and hope that helps.