Maybe I'm being patronize and you know all this all but I'll just note that a protocol is about one level of abstraction above a class library.

I'm biased because I'm working with c++ but I'd suggest the protocol be developed like most protocols - in a language neutral fashion. This involves writing it in a fashion akin to an abstract language. Normally, such a protocol spec simply say what byte means what and where each byte goes. Then the protocol can be implemented in any language.

For example: http://en.wikipedia.org/wiki/Http

Also, I'd suggest only creating a new protocol for things that really can't be done existing protocols (such as Internet mail). You always layer your application on top of an existing protocol if it serves your purposes.

Nothing about the protocol is PHP-specific, but the initial implementation is written in PHP.