Implement your own SMS-based two-factor authentication via the Twilio API.
The Clef service provides an interactive, easy to implement two-factor solution.
The Yubikey USB hardware token makes two-factor authentication as easy as pushing a button.
The Google Authenticator smartphone application makes two-factor auth simple, even without a connection.
Using the Duo Security API you can manage multiple users and integrations, all through a REST interface
Using the Authy REST API, you can quickly and easily integrate two-factor auth into your system.