Protocol Buffers springs to mind. It's a compact binary protocol with 
predefined field order, allowing you to skip unused fields and maintain 
backwards compatibility. You could probably use it as a storage format too. 
It's not in the Lex/Yacc territory, but it DOES generate all the code you 
need to handle the defined structures.

Protobuf is the message definition, and it goes hand in hand with gRPC to 
generate client code plus server code stubs for secure network 
communication with optional streaming:
https://developers.google.com/protocol-buffers/
https://grpc.io

If you're looking for tools for existing binary formats, I dunno. Protobuf 
would only be halfway there, as I don't think it supports unions with 
overlapping fields as you could find in some (like the PE binary format for 
Win32/Win64).

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