Run script before restart/shutdown
You can use a logout hook:
sudo defaults write com.apple.loginwindow LogoutHook ~/.logouthook
echo $'#!/bin/bash\napachectl stop' > ~/.logouthook
chmod +x ~/.logouthook
The value of the LogoutHook key can only be a path to an executable and not a shell command. The logout hook is run with superuser privileges so you don't need sudo.
The defaults command modifies /var/root/Library/Preferences/com.apple.loginwindow.plist. Adding a LogoutHook key to /Library/Preferences/com.apple.loginwindow.plist doesn't work.
If a logout hook takes long enough to run, a gray screen is shown until the logout hook terminates. There doesn't seem to be any time limit after which logout hooks are forced to terminate.
Logout hooks were deprecated in 10.4, but I haven't figured out any way to run programs on logout reliably with launchd. I haven't gotten rc.local.shutdown to work either. I don't know any way to run a logout hook before shutting down or restarting but not before logging out.
If you want Apache stop starting from your computer on boot you probably want to unload the appropiate .plist with launchctl:
Open a terminal, thensudo launchctl unload -w /System/Library/LaunchDaemons/org.apache.httpd.plist