I have write a sophisticate system in php5 (many classes that use static method and include other files)
Now I want to distribuite that ant i would choose the module way
Take a look at hiphop:
Developed at Facebook, and project / code hosted on Github. Will convert code into C++, it depends on what you are trying to achieve, if it is protecting you intellectual property I would agree with duskwuff, Ioncube or ZG.
Worth noting is that once converted with hiphop, the result is not run as an Apache module but rather using a proprietary server also written at FB; well from what I have read so far.