Binary files are standard HDF5 files. These files are in a very compact, non-human-readable format, and are thus very rapid for MODELLER to access. However, unlike some binary files, they are machine-independent (e.g., they can be moved from a Windows machine to a Mac or a Linux box without problems). They can also be accessed using standard HDF5 tools.
Note that the binary files used by MODELLER 8v2 and earlier are not compatible with the current format. If you have any such files, they must be regenerated from their corresponding text files.