Arch Linux

I'll do up a more detailed document but I followed these instruction
https://wiki.archlinux.org/index.php/Google_Authenticator

Install yaourt if not already installed.

pacman -S yaourt

yaourt -S google-authenticator-libpam-git

Note: You will need to edit the build and change the kernel from x686 and x386 to all

Raspbian

The following enforces 2 factor authentication for SSH log-on's and not for the console.

apt-get install libpam-google-authenticator

vi /etc/ssh/sshd_config

on line 48 change ChallengeResponseAuthentication to yes.

ChallengeResponseAuthentication yes

vi /etc/pam.d/sshd

add the following line to line number 15

auth       required     pam_google_authenticator.so

You can add the line to line position number 9 if you prefer the auth code asked before the password.

Run google authenticator to setup authentication.

google-authenticator

Restart ssh service to enable new settings

service ssh restart