Just a quick note. As part of the integration work I did getting YubiKey to work with Alfresco, I also added support for signatures and making validation queries in parallel to the Yubico Java client (I forked the original client) so it should now work with version 2 of the validation protocol; see this FAQ. Hopefully I didn’t fork it up!
You can grab it from my GitHub account: https://github.com/sbuckle/yubico-java-client
If you do decide to use it, you might want to pick and choose which bits you want to pull as I have made other changes not related to the enhancements in version 2.0 of the validation protocol. Now I wonder if I’ll get my five free YubiKeys 
Update: I did. Just ordered them. Thanks Yubico 
