Just to be clear that we have the same issue:
On my machine, if i select 'Restart' or 'Shut Down' from the Apple menu, it quits all of the running applications, as in a normal reboot, but then it simply stops.
The Dock is still accessible, but nothing else happens (i even tried to leave it for 3 hours, with no change)
In fact, i can launch Terminal (i have it in the Dock), then, in sudo mode, type reboot and it'll finally reboot..
Note: i've compared the Console log of the machine in question with one that is not exhibiting the problem, and i think i've found the culprit:
the application 'Install in Progress' seems to start as soon as i click 'Restart', but there are no updates to install...
I'm pretty sure that this is what is happening: for some reason, 'Install in Progress' seems to think that there are updates to run, and it just hangs there, and hangs the whole system with it...
I have tried clearing the caches (using the shareware Cocktail), to no avail..
If anyone can figure it out, please help! It is driving me nuts!!
PS: there are no other error messages in the logs, and i can find no log or preference file that is associated with the application 'Install in Progress' (itself located in /System/Library/CoreServices)