When talking of two factor authentication we need to be aware of reliable hardware and the creation of the key material.
Many known hardware vendors use preseeded hardware, which can easily lead to compromized key material. This hardware is often accompanied by closed source software solutions provided by the hardware vendor.
privacyIDEA is an open source software, which you can run on your own system and use to initialize, manage and authenticate many different kind of authentication devices.
It is ment to give you full control over your authentication process, your accounts and your data. It can be used with standard software using common protocols like RADIUS and PAM and utilizing the lean REST API you can integrate it into your own web applications easily.
This talk gives you an overview over the features and current development ideas.