We are beginning to use petri nets to model our workflows in [OpenACS]. 

If you want to know why, this[http://wwwis.win.tue.nl/~wsinwa/jcsc/jcsc.html] is a good place to start reading.

I found a nice, free Tk petri net editor/simulator here: http://www.laas.fr/tina/ 

-- [PS]