Since we manage our servers with Puppet, we use hiera-gpg to securely store sensitive information in encrypted form in git. Puppet then safely deploys these files to our servers and our application deployment process (Capistrano) symlinks/copies these config files in to the application as part of the deployment process. The sensitive config files themselves are excluded from our application's git repository and developers keep local copies of these files (containing local dev. credentials only) for development purposes.
More info on hiera-gpg here: http://www.craigdunn.org/2011/10/secret-variables-in-puppet-...