Platonides ran apt-get remove wikimedia-task-appserver on bastion which wiped the symlinks out in /usr/local/apache and broke all the wikis.
I re-added the symlinks for /data/project/apache to /usr/local/apache and /data/project/apache/common-local to /usr/local/apache/common which brought the wikis back.
The thumbnails, however remain broken - the below error message is displayed;
Error generating thumbnail
wfStreamThumb() The source file for the specified thumbnail does not exist.
The symlinks /data/project/upload6 to /mnt/upload6 and /data/project/thumbs to /mnt/thumbs seem to be in place and $img->getSource() returns a path which matches that in upload6 (so the image should be there), it's however apparently not.
Looking over CommonSettings.php everything is pointing to the right place and exists where it's expected to be.
I'm not that huge on mw so not too sure where to look next, might just be a squid cache or something silly (though even then I have no idea how we standardly purge thumbnails!).
Shouldn't cause too many issues over the weekend, but we probably should fix it :)