UML
Unified Modelling Language (UML) is a way of documenting the design of an object oriented program. You may find this useful in documenting your Java projects.
UML shows the classes and objects, including their methods, variables and how they interact.
Introduction to UML
For a tutorial on UML got to http://www.tutorialspoint.com/uml/uml_tutorial.pdf
Adding UML to Eclipse
You may find it useful to add a UML editor to your Eclipse. If you browse to http://www.umlet.com/changes.htm you can download a file which can be unzipped and saved into /eclipse/plugins on your computer. This will add the plugin and allow you to create UML documents within Eclipse.