On the PerishablePress.com site there's a recent article showing you how to encode your PHP project's code (though some of the methods are more obfuscation than actual encryption).

There are many ways to encode and decode PHP code. From the perspective of site security, there are three PHP functions - str_rot13(), base64_encode(), and gzinflate - that are frequently used to obfuscate malicious strings of PHP code. For those involved in the securing of websites, understanding how these functions are used to encode and decode encrypted chunks of PHP data is critical to accurate monitoring and expedient attack recovery.

They show examples of several methods of encoding/obfuscation of the code including rot13, base64, gzinflate/gzdeflate and links to some other resources.