I've seen it depicted by Prussia, The Holy Roman Empire and the Byzantines. What is the origin of this symbol and where was it first seen as a standard?
The eagle was a symbol of ancient Rome. There's some discussion on it here: https://www.reddit.com/r/AskHistorians/comments/2zgzh8/howwhy_did_the_eagle_become_the_symbol_of_rome/
Clearly, Byzantium is the continuation of the Roman Empire in the east. Frederick I, Holy Roman Emperor, adopted the Eagle as a symbol of the Empire in 1155. I can't seem to find the date that Prussia (or potentially, the Teutonic State, as pre-cursor to Prussia) adopted the eagle as its coat of arms. Let me know if you're interested and I'll hunt around for it.