Currently Being ModeratedFeb 11, 2013 2:32 AM (in response to Darkfortress1)
Both Lion and Mt Lion indiscriminately reopen programs that were left open when the system was shut down or restarted. Even with the option on the shutdown screen for that to happen is unchecked.
So make sure you have actually closed all program, not just closed the windows they were using, before you do a shut down and restart. You can do that in 2 ways.
If the App has a little White Dot next to it in the Dock then it is still open. Right click on that app and select Quit.
Bring up the Force Quit dialog window and select the app and click the Force Quit button.
Then reboot and see if they still open. If they do then you have them in the Login Items section of User & Groups in Sys Prefs, Remove them from there.