In a new post to his blog Johannes Schluter recommends that you don't use references in your applications, mostly because of some misconceptions about how they work.
Last year I spoke at eight conferences and attended a few more multiple times at most of them I found myself in discussions about references and PHP as many users seem to have wrong understandings about them. Before going to deep into the subject let's start with a quick reminder what references are and clear some confusion about objects which are "passed by reference."
He re-introduces referenced variables and scratches the surface about the confusion they can cause, not only on the user level but also in the internals of the language, and can lead to some unexpected results. He also mentions the "always passed by reference" idea that several PHPers have about PHP5 objects and why it's not entirely correct. He finishes off the post with a look at returning referenced parameters and how it can lead to bad application design.