Previously I wrote about my intent to use phpDocumentor on a project. I have since switched to using ApiGen. Gradually I became less happy with the formatting of phpDocumentor’s output. You can customize that but honestly it was easier to switch to another tool than to setup a theme that I wanted. ApiGen already understands all of the annotations I was using, so I had to change nothing within my code. And in my opinion its output is easier to read and easier to browse.
I am going to stick with ApiGen, while a friend is going to use phpDocumentor instead. If you’re writing any PHP software then give both a shot and see which one works best for you.