In this recent post to his blog Philip Norton shows you how to get started with DocBlox, the "new defacto PHP class documentation generator" that recently announced it would be merging with the phpDocumentor project in version 2.
Whereas PHPDocumentor would scan and generate all of the code in one go, DocBlox will scan the source code and generate a series of XML files based on the code it finds. It will then use these files to generate the API documentation in a number of different formats, although HTML is probably the most common.
He points out a few packages that you need to have installed before continuing (PHP-XSL, Graphiz, PEAR) and the commands you'll need to get it installed via the PEAR installer. He shows the commands to generate the documentation, how to install different template types and set up a configuration XML file.