Use a package like sync-settings. This will store your configuration in a GitHub Gist.
Dropbox (or similar): Move your ~/.atom folder to your Dropbox folder and then symlink it from there to its original location. This has the downside of syncing everything in ~/.atom, even the things you could ignore.
Use stars to select your favorite packages. On the Atom web site, create an account and mark your favorite packages with stars. Then use apm stars --install to install all starred packages on any machine. Downside: This only works for packages, not for settings.