For those looking for Google Authenticator alternatives, I recommend either Duo Mobile from Duo Security or Authy. I ditched Google Authenticator a while ago and haven't missed it one bit -- having a single app manage my two-factor tokens / keys is much more convenient.
Duo does not require this at all. And Authy only requires you to store their "Authy" token. You can add additional, e.g. Github, tokens to Authy and choose not to sync them with the Authy servers. That's what I do.
Authy requires your mobile phone number and the creation of an account to work at all … or am I missing something? I haven't found a way to use Authy without providing my mobile phone number and creating an account.
I second the recommendation for Duo. Its a great application, and if you're looking for adding 2FA to your own systems (IT or otherwise) has a multitude of interaction options (secondary password LDAP, etc).