Jason Sweat has slides from a presentation titled “Documenting PHP Applications” that he gave at PHP|Works in Toronto. I wish I could have seen the presentation, the slides are great.
If your new to phpDocumentor reading the slides is a great place to start. He does a great job of showing off the basic features, and gives some nice examples of the code -> document path. Made me feel like Jason knows more about phpDocumentor then me :-|.
On a slightly related note, there are some people having problems running phpDocumentor on OSX if someone runs it and would be willing to help debug, I’d be greatful.