has someone a solution for a simple and affordable two factor authentication for RDP similar to the SSH login on a unix machine?
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PhoneFactor might do the trick:
If you use Radius for authentication, all the major two-factor authentication systems are options for you. You probably need to run the RDP through ISA.
Here's a tutorial I wrote some time ago: http://www.wikidsystems.com/support/wikid-support-center/how-to/how-to-configure-the-microsoft-isa-server-to-support-two-factor-authentication-from-wikid. Note that IAS has been replaced by NPS in 2008+.