The phpDocumentor tool is a standalone auto-documentor similar to JavaDoc
written in PHP. It differs from PHPDoc in that it is MUCH faster, parses a much
wider range of php files, and comes with many customizations including 11 HTML
templates, windows help file CHM output, PDF output, and XML DocBook peardoc2
output for use with documenting PEAR. In addition, it can do PHPXref source
code highlighting and linking.

Features (short list):
-output in HTML, PDF (directly), CHM (with windows help compiler), XML DocBook
-very fast
-web and command-line interface
-fully customizable output with Smarty-based templates
-recognizes JavaDoc-style documentation with special tags customized for PHP 4
-automatic linking, class inheritance diagrams and intelligent override
-customizable source code highlighting, with phpxref-style cross-referencing
-parses standard README/CHANGELOG/INSTALL/FAQ files and includes them
directly in documentation
-generates a todo list from @todo tags in source
-generates multiple documentation sets based on @access private, @internal and
{@internal} tags
-example php files can be placed directly in documentation with highlighting
and phpxref linking using the @example tag
-linking between external manual and API documentation is possible at the
sub-section level in all output formats
-easily extended for specific documentation needs with Converter
-full documentation of every feature, manual can be generated directly from
the source code with "phpdoc -c makedocs" in any format desired.
-current manual always available at http://www.phpdoc.org/manual.php
-user .ini files can be used to control output, multiple outputs can be
generated at once

WWW: http://pear.php.net/package/PhpDocumentor/