Volker Dusch has a new post to his blog looking at the use of references in PHP (or lack there of) and what we, as end users of the language, can do about it. His example looks at mysqli prepared statements.
Even so not every PHP Developers knows WHY we don't use references pretty much every core function and every somewhat modern framework avoids them so people adapted this best practice. The leftovers in the PHP core, like sort() or str_replace(), are exceptions to the rule. So if the common consensus is, or at least 'should be', that we should not use references then maybe we should start looking for places where they hurt and how we could fix them?
He talks about prepared statements and one thing he sees that makes it a "hard sell" to developers needing a good way to query their databases. He points out the difference in code required between the normal MySQL calls and mysqli (hint: it's more) and shows how to use an abstraction layer to make things a bit easier. He points out the downfalls of using this approach, mainly the performance hit you get (from using his fetchAll method).