phpDocumentor is the current standard auto-documentation tool for the
php language. phpDocumentor has support for linking between documentation,
incorporating user level documents like tutorials and creation of
highlighted source code with cross referencing to php general
documentation.
phpDocumentor uses an extensive templating system to change your source
code comments into human readable, and hence useful, formats. This system
allows the creation of easy to read documentation in 15 different
pre-designed HTML versions, PDF format, Windows Helpfile CHM format, and
in Docbook XML.