This is an old topic - but in case anyone finds it useful....
kKCachegrind will produce callgraphs shown the actual execution threads.
PHPCallGraph is a fairly simple around graphviz which perfroms static analysis
There's also my own effort which is similar to PHPCallGraph but adds information about loops/conditional structures and provides a method for adding callbacks to nodes. Some example scripts are bundled with the toolkit - but you can also embed it in your own scripts.
