We have deleted that feature, which we had in Yubikey 1.x. Partly for security reasons (although anyone who don't like it could turn it off) but also for compatibility reasons. This function really functioned on Windows platforms only.
Without knowing the needs in details, have you considered the new challenge-response functionality, provided by firmware version 2.2 ? Here, you can programmatically send a challenge to the Yubikey and optionally wait for the user to press the key. The challenge is then processed by the Yubikey and you get a response back. This however, contrary to the general Yubikey paradigm, requires client-side drivers.
We have deployed a Windows library and some sample applications to test these features out. Please check it out at
http://www.yubico.com/personalization-tool/There, installers and user guides form the Client- and Server APIs can be downloaded for evaluation.
Regards,
JakobE
Hardware- and firmware guy @ Yubico