Taking a look at the output from atop, I saw that apport was running and taking 100% CPU (user mode). This was apparently enough to freeze all of the other processes such as X11 and Firestorm and Skype and Chromium and XFCE and the rest.
I killed apport and lo! everything returned to normal.
Researching this shows that a bug was reported way back in 2008 with Hardy, and remains present in 2012 in Precise Pangolin (and here it shows on my Vivid Vervet system). The problem occurs when apport is enabled on a “production” system such as a user’s desktop, instead of a machine being used for development of the Ubuntu distribution.
To disable it, go into the file /etc/defaults/apport and change the appropriate line so it reads:
That will disable apport so it won’t run on boot. The next step is to actually stop it entirely with:
service apport stop
If you really want to make sure everything is clean, you can reboot instead. This way, apport never starts at all, nor anything that depends on it.
If you want to go all out, you can remove apport entirely with:
apt-get remove apport
If you purge it, your configuration files are removed too – but by just removing it, you have a greater chance that apport won’t be enabled on an upgrade. If you upgrade from one distribution version to another, it might be re-enabled.
Another thing you may wish to do is to clean out the crash directory. The utility apport reads the crash directory and has been known to hang there. Cleaning it out may help in the event that apport winds up running and hangs. Clean it out with:
rm -f /var/crash/*
Hopefully, this will help you resolve any apport issues.