graphviz is a great tool for creating quick diagrams. While it does not have a particularly polished WYSIWYG editor such as omnigraffle, it can automatically create diagrams from its simple markup language, DOT. After reading in the DOT markup, it uses various layout algorithms to automatically arrange the diagram. The DOT language is pretty flexible in its formatting and quite easy to generate from other programs.
The main installation includes a couple of standalone programs, such as
neato. I’ve mostly used
dot, which creates directed graphs. (
neato renders undirected graphs.) While installing it is beyond the scope of this post, installation is straightforward on OSX, Windows, and most Linux and BSD distributions.