For now I am going to use iteration path to capture the version number. This doesn't lend itself so well to managing development on different versions concurrently, but we are trying to get away from that practise (i.e. be working on the next release while simultaneously working on multiple bug fixes to past releases) and adopt short release cycles, i.e. a more linear path, so maybe that is a good thing.
Earlier I though Area Path might be a good place to put Version, but its too valuable as a way to split up a huge application into parts to sacrifice for versioning.