Strange things were afoot this evening when I switched on my laptop. Ubuntu did the intermittant "HAL could not be initialized" error first of all. A quick reboot and everything seemed ok for a couple of minutes. The update indicator was red so I though I ought to do a quick update. As that was processing suddenly it produced a nasty error stating that I needed to run "dpkg --configure -a" manually to set everything straight. Next the terminal wasn't firing up so I thought I'll just do a quick reboot.
As the shutdown was happening I saw lots of error messages about readonly filesystem which didn't look good. Subsequently when I started everything up again the filesystem was screwed. An automated fsck failed and the error message said to run fsck manually without any switches. I logged in as root and ran fsck and then said yes to fixing everything it found. After this was finished I shut down and rebooted only to find that X died straight after login! I tried a few times but no joy so I then rebooted once more. This time everything was ok and I got into the desktop.
I then thought I'd go back to the updates as they were where the trouble had started. I tried to run the updater but I got the same error as before. I then opened up a terminal and ran "dpkg --configure -a". Next I re-ran the updater and everything went fine. Finally I was back to stability.
The one thing I will say is that all of the messages the operating gave me regarding what was needed to be run manually was sound advice and eventually saved me further recovery attempts.