Document Generator Tools

One of the popular Document Generator Tools for PHP are listed below:

DoxyGen
Source code documentation generator tool
Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
(It's used by Drupal as well I guess, so this one should be definitely one of the Bests):
http://www.stack.nl/~dimitri/doxygen/

phpDocumentar
http://www.phpdoc.org/