As an illustration that a graph can obfuscate things instead of helping is my graphing of the perl grammar. I have done that before Leon Brocart wrote his modules. He once used that graph to demonstrate the capability of graphviz. Clearly, "strongly" connected graphs are not very readable.
But Doxygen uses graphviz pretty well. I use it to navigate thru the TeXmacs sources. click any class name to see such graphs.