Standards

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There are various documents detailing how different bits of the desktop work:

Configuration system: Describes where to load and save user preferences and allows layers of preferences (such that user preferences override system-wide preferences and so on).
Application directories: A system for distributing applications in a form that can be run without the need to install anything. The application program remains completely self-contained.
Freedesktop.org: The X Desktop Group has links to various standards that are common to several desktops, and develops new ones. Lots of interesting work is going on here.
The X Direct Save protocol: This protocol allows the user to save by dragging data from a program to a filer.
There is a test application here: http://rox.sf.net/xds.html