I've upgraded from 11.04 to 11.10 and now I am missing the majority of files in /run (my other 11.10 machine has 44 files/folders in /run while the broken system has only 11).
One of the main missing folders is /run/network which makes my networking not work on startup.
Also, possibly related when I do a normal boot I get a blank X screen with an X cursor. After killing X and doing a manual startx, X loads rather well, I can see notifications from notifysend (such as guake and dropbox) and can run some X programs (my autostarted synergy works well).
I should mention that my upgrade did not go smoothly and did something like give an error that the upgrade did not complete successfully, followed by a message that my upgrade did complete successfully.