If and when things fall apart:

Training for endurance events can lead to repetitive stress injuries and, for those interested, a much greater knowledge of how the body works and doesn't work. Here are some methods, ideas, and treatments that have helped me.

Prevention:

Rather obviously, it's best not to get injured in the first place. Strength training, range-of-motion work (stretching is overrated), and smart training are the basics.

Trigger point therapy:

It seems oftentimes the area that hurts is not the problem. A book that has been incredibly helpful to me is Clair Davies book on Trigger Point therapy. It's essentially a reference book: look up the area that's in trouble and work your way down through the possible causes.

Davies's book is a simplified version of Travell and Simons's two volume medical reference Myofascial Pain and Dysfunction: The Trigger Point Manual. The drawings and detail here are wonderful.