privacyIDEA is a management and authentication system for two factor authentication. You can use OTP tokens, OTP cards, SMS, Smartphone Apps to incorparte the second factor.
Its modular design makes it easily enhancable. It runs on Linux.
Applications and workflows can be connected to privacyIDEA hence enabling two factor authentication in your system logon, web applications, SSL VPNs, firewalls and many more.
A detailed audit log gives you full control of what happens when, where (why? ;-) and by whom.