Just a quick note to remind myself, when I inevitably forget.
The built-in GnuPG smartcard support doesn't really work particularly well, in my experience, with the YubiKey Neo. To fix this (and use pcscd) instead, put the following in ~/.gnupg/scdaemon.conf:
pcsc-driver /usr/lib/libpcsclite.so
card-timeout 5
disable-ccid