Doxygen is very good at generating diagrams from code without applying markup, if you turn on the EXTRACT_ALL option. You need GraphViz installed to get diagrams generated with the HAVE_DOT setting. I find having it installed and leaving the DOT_PATH blank works fine on Windows but on OS/X keep having to point directly to the dot tool location.
There's an excellent Code Spelunking article in ACM Queue which talks more about using doxygen and DTrace.
