I always worry that adding 2FA could make your machine inaccessible if anything happens to google-authenticator in this case. Maybe it's a little bit of paranoia but I don't like the idea of giving control over my ability to log into my server.
Speaking of TOTP without Google, if you use iOS and find the Google Authenticator app unsatisfactory, try Authy. It's good stuff, and well worth a few bucks.
OTP Auth is another excellent, free OTP client.
Edit: clarified both are free.
no beer required :-)
I use the desktop app every day and am generally happy with it. It has many thoughtful touches, like automatically clearing the clipboard a minute or so after you copy a password into it, so that you don't later paste your password into some other text field by accident.
It's of course open source.