Same thing occurring to me. My MacBook Pro 13" Late 2011 with Mountain Lion (10.8.5) sometimes hangs for 20~30 minutes at boot, in verbose i can see that this occurs just after the "FIPS USER Space POST: Success!" message.
I dont use any anti-virus, firewalls or "clean my mac" kind of apps.
One week ago i traced the problem to a very strange situation, the hang usually occurs when i use the NetBeans 7.3 app in the session just before the reboot. Cant explain why it happens, but since i stopped using NetBeans the problem seems to have gone away.
This started happening to me each time I tried to boot my Mac.
I have a MacBook Pro OS Mountain Lion v10.8.4
It's not "stuck" on reboot, but just extremely slow. It would take between 3 minutes to 50 minutes to boot (I booted through Verbose mode). I had tried Verifying/Repairing disk, but it was always "ok", never any errors/fixes needed.
How I Fixed it:
1. I removed 2 Applications with AppCleaner that were recently added to my Mac prior to this problem.
They were Sequel Pro and Monosnap.
2. I had an app (xCode) that it's update was only partially installed, it had been paused. I completed installing the update.
3. I then updated my OS from 10.8.4 to 10.8.5
4. Restarted, and the problem was gone.
I hope this helps someone else, as I was freaking out everytime it happened to me. I do believe its a problem with an application slowing down the boot, in my case, I believe it was Sequel Pro.