Sorry for reviving an old thread.
I'm in the process of trying to transition from being a solo developer (with my own quite poor code commenting and documenting!) to working with other developers so need to be more disciplined and use better tools. I'm now using GIT and Bitbucket for version control but need to improve my documenting too. Is PHPDocumentor still the go-to app for documenting PHP code or are there better alternatives now in 2015?