I recently have had to generate a PHP project’s documentation and I’ve chosen the popular PhpDocumentor for this purpose.
This tool is unfortunately outdated, hasn’t been updated since 2007, and thus throws a lot of PHP warnings and cannot do what I was asking it.

My friend Ludo has suggested using DocBlox which is, compared to PhpDocumentor, more modern - supports PHP 5.3, faster, and consumes less memory.

After trying it, I can say that it’s indeed a great tool, inasmuch as I could generate documentation for my project 5 seconds after installing it.

How to use it:

Installation

Make PEAR know about DocBlox’s channel

pear channel-discover pear.docblox-project.org

Then install DocBlox(-beta)

pear install docblox/DocBlox-beta

The command line docblox should be available for use now.

Use

docblox -d /path/folder1,/path/folder1/folder2 -t /path/to/target/directory

Easy, ha? :)

Make sure you separate the source directories by commas only, no spaces.
You can also use some of the basic PhpDocumentor commands.