Also missing: the system dynamics paradigm, where boxes are accumulators and arrows are flows. Many packages like this have existed and still exist.

This is (a recent iteration) of Stella: http://sdwise.com/wp-content/uploads/2013/11/System-Dynamics...

Here's VENSIM: http://www.makrosimulation.de/Screenshot-Staatpublish.jpg

Matlab's SIMULINK is kind of a generalization of this paradigm (less convenient because of too many choices to make): http://ctms.engin.umich.edu/CTMS/Content/Suspension/Simulink...