System Login
No real guide on best practices here yet.
For the moment take a look at the following for (unverified) research others have done:
OSX
https://www.yubico.com/why-yubico/for-businesses/computer-login/mac-os-login/ https://blog.avisi.nl/2014/05/06/two-factor-authentication-on-osx-a-yubikey-example/ https://crewjam.com/yubikey-for-local-authentication-on-mac/
Qubes
https://www.qubes-os.org/doc/yubi-key/
Linux
https://z3ntu.github.io/2016/07/23/SDDM-login-with-yubikey.html http://askubuntu.com/questions/635266/use-of-yubikey-neo-for-login-2fa-and-lock-screen https://blog.rootshell.be/2009/03/27/yubikey-authentication-on-linux/
Windows
https://www.yubico.com/why-yubico/for-businesses/computer-login/windows-login/ http://www.rohos.com/support-old/knowledge-base/windows-logon-with-yubikey/
OpenBSD
https://www.jfry.me/articles/2014/openbsd-yubikey/