You can store a lot of information with your diagram using the Data Property inspector. The cool thing about storing at least some of this information is that it is available in the Spotlight indexing feature that comes with the Macintosh operating system.
If you do not care for Copyright, Version, Subject, or long and windy Comments, at least fill out the Description field. As your collection of OmniGraffle diagrams grows on your computer, finding the right diagram after a few months will become both tedious and very time consuming.
You can also, by the aid of the drop-down menu, add Authors, Organizations, Languages, Keywords, and Projects.