I have Ubuntu 9.10 installed on my HP desktop, but I'm running an older version (8.10) on a live CD so I can at least get online to ask for some help.

When I tried to log on earlier it went to a command prompt and said the 'file system check failed' and to run fsck manually. I entered 'sudo fsck' at the prompt and I selected "y" to fix all the bad inodes, when it was complete it told me to restart, I then entered 'sudo restart' at the prompt and it said 'sudo uuid unknown'. I have not installed anything recently and I'm not sure what to do.

Have you tried rebooting? What happened?
Have you tried examining the content of your HDD from the live session?

I have tried rebooting several times without any luck. At the grub screen I just tried to boot the most recent kernel listed after removing the 'quiet splash' from the end of the line. I received the following error 'Failure: AppArmor profiles failed to load'. I can get to some of the files on my HDD but I don't know what to look for.

If you can mount your HDD, and get to the files, then you can recover. Just copy the files you want to keep someplace else - reinstall - copy them back.

That does not normally stop the boot process. How far does it get?

Will it boot into rescue mode?