Some of the new PHP 5.3 features, including namespaces and anonymous functions, are not compatible with PHPDocumentor, even with the latest release. For example, it just raises
You could try DocBlox; which is intended to be an alternative for phpDocumentor but with support for additional features of which full PHP 5.3 support is one. An additional benefit is that is it quite fast and uses relatively little memory.
You can read more on http://www.docblox-project.org or see a demo at http://demo.docblox-project.org/default