I've used the libpam module for Google Authenticator[0] before, the difference being that it isn't dependant on the availability of a third-party service, but you have to be much more careful about losing your device. That said Authy do have pretty great uptime[1]
Nice for production servers, but becomes a an annoyance after the cool factor wears off for servers that don't really need it :) Installable on aptitude using libpam-google-authenticator (guide [2]).