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
This was already mentioned in a comment by @mvriel, but I'll make it an answer: phpDocumentor's successor is phpDocumentor 2. From its website:
phpDocumentor 2 is build to generate API documentation for all features available in PHP 5.3 and higher.
phpDocumentor 2 is the result of the merge between phpDocumentor and DocBlox. From the merge announcement in DocBlox's website:
Announcing phpDocumentor 2 – the merging of the old (phpDocumentor) and the new (DocBlox).
...
Old phpDocumentor is retiring. Some bugfix effort may continue into bringing phpDocumentor 1.x to a close, but most effort going forward will be spent on 2.x.
It's still in alpha stage (as of 2013-04-01), but usable.