I've started a project over at Google Code, so anyone can lend a hand or view the code. The project aims to be a simple set of classes for PHP that help you write your own Yubico Yubikey authentication systems. For instance, I intend to integrate my work with my OpenID provider so that I can easily ID myself online.
As soon as my key arrives in the mail, I will be able to test things a bit better. Yubico has set up a forum, but, alas, you need a Yubikey to post. However, reading is free, so I would suggest that those interested check out the server side forum for more details.