Emacs native backups
By default, Emacs will save a backup file on first write of a file buffer. Backups should be omitted for files which are checked into version control. They can be made by renaming or copying the source file. This choice has implications for hard links and ownership.1 Copying seems to be the safer option.
While many people seem to prefer sending all backups to a separate directory, the default behavior of storing them alongside the source files strikes me as a reasonable minimalistic approach. It makes it easy to tell when a backup has been created. Furthermore, these backups will be retained if the parent directory is copied/moved.