Probably waiting for some or other process to end. Do you choose Reboot/Shutdown when all your apps are closed and just the Finder's active or in the middle of having everything open?
If you have closed every application, you might want to check Activity Monitor to see whether some background processes still use a lot of the CPU(s).
Also: Repair permissions (using Disk Utility), reboot and try again...
If that doesn't do the trick, try creating a (empty) new user profile, boot into that and reboot again. See if it's much faster.