Is there some mining software out there that doesn't use Json-RPC as a communication method with the mining pool? If so, what protocol are they using?
JSON-RPC is simple and effective. I think most use it.
If people would change it, it's most likely for efficiency. They'd most likely roll their own binary protocol, which we might very well know nothing about.
It's also possible the miner is inside the client in which case it could get it's own work and wouldn't even need a protocol.
If you could say why you want to know maybe I can give a more useful answer.