bytecode caches (like APC) store the bytecode on the fly in memory. you can't create somthing like a "binary" file.

edit: at least they're not intended to create "binaries". you can probably mess around with APC and make php look and behave like a compiled language. but you won't gain any notable speed improvements beyond the on the fly caching.

edit2: you can store php projects in a jar like file, caller phar. http://php.net/phar