On PHPMaster.com today there's an article with some good suggestions about ways to deprecate parts of an API safely.

Deprecation can happen for various reasons – perhaps an API is no longer useful and has reached its end-of-life, or the refactoring of code to improve its reusability and testability obsoletes particular methods. In this article I’ll share with you some key points that you should follow when deprecating APIs so you can continue to grow your code and provide fair warning to those who depend on it.

They break it up into a few different steps:

• Prepare for Refactoring
• Employ the Single Responsibility Principle
• Communicate with your Users
• Remove the Old Code