Personally I think many of the desktop file formats of the 1990s were systematic, disciplined and well designed. Feel free to differ but I'll say PDF (object graph with containers that can hold more nodes) and Microsoft Office (object serialization and dynamic loading of the libraries to work with the objects, even to visually interact with the objects) are stand outs.

But PSD files are crap, probably because they're just a little bit older. I can only imagine what was going through the mind of a team that was getting something to work on both big-endian and little-endian architectures, it sure wasn't "standardize on one"