Best way to do this is to obfuscate your source files.

IONCube:
PHP Encoder, protection, installer and performance tools from ionCube: ionCube PHP Encoder

Zend Guard:
Zend Guard - Protect Your IP & Generate More Revenue - Zend.com

Those two are what most people use, although they are quite expensive. There is however a free alternative:
Free PHP Encoder - Free PHP Code Encryption and Obfuscation Service!

Don't know how good it is or indeed how secure it is, but it should stop most of the muppets.

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mysql> SELECT * FROM `users` WHERE `users`.`clue` > 0;
Empty set (0.00 sec)