Oddly I have an installation of Emacs on my current ArchLinux box that doesn't shut down with `C-xC-c`.... I've had to resort to `C-z, ps ax | grep emacs` to kill the process. I haven't cared enough to fix it.
So in this case, `M-x save-buffers-kill-emacs`, or simply `M-x kill-emacs`, could have done the job.
(if this still didn't work, you could even have written "(kill-emacs)" in a buffer and ran it with `C-x C-e` :D )