The post the explained it best, in my opinion, was from vreference.com where Forbes Guthrie explains it. To sum it up, reboot and halt, does not execute the kill scripts. They just unmount the file systems and either reboot or stop the system. You are best off using the shutdown command to reboot or shutdown the system.
Forbes says this about what to use:
"So, should I use reboot or init 6? – neither! My advice is to use the shutdown command. shutdown will do a similar job to init 6, but it has more options and a better default action. Along with kicking off an init 6, the shutdown command will also notify all logged in users (logged in at a tty), notify all processes the system is going down and by default will pause for a set time before rebooting (giving you the chance to cancel the reboot if you realize that you made a mistake)."
So using shutdown is a good habit I am going to have to get into.