Bob Bringhurst, the lead writer for InDesign and Incopy at Adobe, has posted a comprehensive list of the "scope" of all of the Preference settings in InDesign. This is great! I've been meaning to research and put such a list together for years...now I don't have to (procrastination pays off)!
The problem is that the various Preference settings in InDesign behave differently. Some affect just the currently open document, and are saved with the document, while others "stick" and remain in effect for all documents. I've filed a feature request with Adobe to add some sort of visual indicator in future versions of InDesign to designate which Preference settings are document-specific, and which are application-specific.