Recently had a similar problem. I started in safe mode and waited, and waited,... after 6 hours (hours!) I had to force a restart by holding the power button.
I expected it to take awhile but that long suggests something wrong. There were also no system logs for that time. After that I started in single user mode and ran applejack to do similar disk checks and that only ran for a few minutes.
I've booted from a USB MountainLion startup disk and used Disk Utilty to verify the disk. Everything is ok.