How is the Blizzard Mobile Authenticator implemented? Does it happen to use OATH-TOTP or something similar?
There's a Windows client at http://code.google.com/p/winauth/ which was made by reverse-engineering the protocol. They refer to http://www.wowwiki.com/Battle.net_Mobile_Authenticator_Specification as a description of the protocol, but it's rather sketchy.
You probably have to read the source to an authenticator to get a full understanding. There's one written in python at https://github.com/Adys/python-bna that would probably be the easiest to read.