I bought myself a YubiKey Neo and it works great on my Linux systems but there's one little snag I hit tonight (and solved).
I took my YubiKey to another computer and wanted to SSH to my server which is configured to let me log in using it as the key. Unfortunately I couldn't get the key to be recognized by gpg-agent.
Doing this: gpg-agent --enable-ssh-support --daemon ssh-add -l
didn't work. No keys were listed (except ones on the hard drive).
Turns out my problem was I needed to install gnupg2-smime.
After the fact I remembered I did that on the first computer I setup to use it.
This is probably your problem if gpg --card-status works but gpg2 --card-status doesn't.