As shown by my practice can best be protected from theft in a legal plane: to formalize intellectual property and to issue client license. Well, in the event of a leak to bother on quite legal grounds.
\r
ionCube, Zend, SourceCop, SourceGuardian, bCompiler in some cases complicate the support for the product as such (there are subtle bugs that are not in a "clean" source).
\r
However, you can use obfuscators source, if not all, then some critical parts.