Thanks for the mention, Tate. This is a great question. I interpret it as "how can I start moving toward stronger forms of authentication." There are a lot of parts to this question and some good answers, some ... still waiting for better answers.
Protocols: Radius, LDAP, SAML, OATH. Radius is great for internal use (ldap is more of a directory protocol than an auth, IMO) and the last two are designed for external/internet auth. Choose an internal protocol and then an external method. Limiting yourself in this way keeps it clean and helps you to learn.
First, ubuntu: that's easy. you just need to learn a little bit about PAM - the Pluggable authentication module. PAM supports a bunch of protocols. Build the library for your protocol and then edit the services files in /etc/pam.d/. So, sshd, login, su, sudo, whatever. Here's a doc on how to add two-factor authentication to SSH: http://www.wikidsystems.com/support/wikid-support-center/how-to/how-to-secure-ssh-with-two-factor-authentication-from-wikid/. Just do the same for login, and you should be good. One caveat: leave a way to get in! You don't want to be locked out. This is one reason why most companies only worry about remote access and not local access.
Windows login: This means changing the windows login or GINA. Do this at your own risk as well. Check out the opensource pgina project. I tested this with WiKID using radius on windows xp a long time ago and it worked great. But none of our customers implemented this because of the risk of lock-out and potential support costs.
Websites: Increasingly companies are separating "login creds" from "accounts" and seeing that they can get more of the latter if they let someone else handle the former. Hooray. However, not all the authenticating parties are doing two-factor auth. Google is the only one. You may not be comfortable with google knowing your every login, though and you might want a server that you can control and use for other services too.
If so, our open-source version includes a plugin for GoogleSSO for Google Domains: http://www.wikidsystems.com/support/wikid-support-center/how-to/how-to-wikid-strong-authentication-to-google-apps-for-your-domain/.
Good luck! HTH,