'maemo' is the name of the whole software platform.
'bora' and 'mistral' are codenames for the software versions of the operating system/user environment: bora is the current version for OS2007 (N800) and mistral is for OS2006 (770). But many mistral packages will work also on OS2007, however if there's a bora version then that's what you should use.
'binary' in this context ususally means the installable application (as opposed to its source code, which is of interest for developers only).