What will prevent a reboot?

Solution 1:

As a general catchall the following items will interrupt a reboot:

• Opening an application during the shut down sequence. It doesn't affect shutdown -r however.
• A stuck process or stuck processes - where a hard reset is most often the quickest (but not safest option). Finding out why a process is stuck can be troublesome at times.

Solution 2:

Well, in my particular instance, this server (an Apple XServe) was not talking to the attached RAID unit. I finally rebooted the server, the RAID unit, and the server again, and thinks worked.

From my research, it appears that tasks can get into the stuck or uninterruptible state, and even SIGKILL will not phase them. I believe that one process was waiting for the RAID volumes to mount, and the other processes (particularly the 'reboot' commands) were waiting for it.