Need to check if anyone had the same issue. Before going to sleep, all my sites were fine. The next day, I found out Wordpress autoupdated to 4.1 (on my multi-site) and all plugins were deactivated, cannot be re-activated and the site was messed up.
Turned out (super thanks to my hosting provider who found the issue) - that the wp_sitemeta was listed as crashed.
141217 18:42:42 [ERROR] /usr/sbin/mysqld: Table './xxxxx_wrdp8/wp_sitemeta' is marked as crashed and should be repaired
They had to repair and seems all is fine now.
Have you encountered same? I better turn off auto-update from now on.