just my 0,02 cent worth suggestion ...
Maybe some files have been corrupted (disk failure) so you are no more able to reboot properly.
Have you tried to reboot off a knopix cd, and then try to check your hd status?
I had a couple of times a similar problem (in the very beginning, when I was making a lot of experiments and system was crashing frequently) and it ended up that the shortest fix was to reinstall pluto keeping data partition.
Obviously if you don't have a recent backup of your mysql tables this may result a bit annoying ..
Regarding backup, you may find interesting this thread
Again, just my 0,02 cent