Two factor options

In some online services specific functions to be carried out present good use cases for adding increased assurance to the authentication of the user logging in to perform such a task, for example to sign domains with DNSSEC or for the approval of Extended Validation SSL certificate requests.

There are many different methods for two factor authentication including hardware tokens, user certificates, SMS text and a standards based Google Authenticator-type system etc. Some of these options can be deployed in a variety of ways, for example the use of Yubikey as a hardware token, or a Time-based One-time Password Algorithm (TOTP) running on a smartphone app or in a web browser plug-in. 

The question I’m interested in is which is the preferred two factor option for those users served directly by Janet, not necessarily end users such as students?

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