Nowadays, phpDocumentor version 2 is probably the best option out there as it has a good architecture, it works fine, it is extensible, and quite a few big PHP projects is already using it. And that's fine. I don't want to compete with it, I don't want to replace it, I'm just open sourcing some code used by Symfony, Twig, and Silex because I'm not comfortable with closed-source software. And to be totally honest and transparent, I have not released the code before because it was not "good enough".
He gives an example of how to install and use Sami - configuring the directories to parse and setting up a custom theme for the resulting generated documentation (using regular CSS and HTML definitions).