I´ll go for doxygen too.
Here are several reasons :
- compatible with phpdoc tags and other popular ones : it´s interoperable
- works with various programming languages : a better time investment
- there is alternative syntaxes : can choose the commenting style that suit you
- very efficient with advanced formating / tagging / metadata
- there is a GUI that is not linked to any IDE and an eclipse plugin as well
And still free, multiplatform, and open source :-)
It´s easy to learn, but harder that phpdoc because a lot richer.
