Seems that the de facto approach is to backup-rm-symlink. My approach is to source from existing configs whenever possible. Specifically, instead of

  mv ~/.bashrc ~/.bashrc.bak; ln -s $DOTFILES_PATH/.bashrc ~/.bashrc

I do a slightly more sophisticated version of:

  echo "source $DOTFILES_PATH/.bashrc" >> ~/.bashrc

(The sophistication comes in checking if that line already exists.)

Here's my install script: https://github.com/shazow/dotfiles/blob/master/install.sh

I've found many benefits in this, such as easily having machine-specific configuration side by side with my unified dotfiles and no backup clutter. This works especially well for things like vim configs, too.

  $ cat ~/.vimrc
  source $DOTFILES_PATH/.vimrc