First the DISCLAIMER: don't take the following for gospel. If you have medical questions, go talk to a physician. None of the people quoted here is a physician.
Joints, in particular knees and ankles
Someone has written an actual FAQ about stretching and flexibility. You can find it at http://www.sunshine.net/www/0/sn0016/ .
The medical multimedia group has information, mostly about joint problems: http://www.sechrest.com/mmg/reflib/reflib.html.