Hi ChrisHurst. When you set up WordPress and your content in separate directories and use version control systems such as git, it is interesting to keep certain directories outside.
For instance, my setup is something like that:
/content (custom wp-content)
/shared (uploads etc)
/wp (default wordpress)
(see WordPress-Skeleton)
So it would be great to have the backup directory in the “shared” directory, which is out of version control (this way, it will not disappear when upgrading wordpress via git).