A single place where I store all my dotfiles, and a handy script to set them up in new environments. Clone the repository wherever you want, then run setup.py. The script will make symlinks to all the dotfiles in the cloned repository, and will make backups of any files before overwriting. If you add any files, make sure to source them in your ~/.bashrc or ~/.zshrc! Updating dotfiles is as easy as pulling from git and re-running setup.py.
If you want custom configurations depending on hostname, put them into the hostnames folder with the filename hostname.install. The setup script will only install the relevant files.