With this BungeeCord plugin, you can customize the /help message per server and much more...
/bungeehelp - Shows info about the plugin.
/bh help bungeehelp.help - Shows all the plugin's commands and permissions.
/bh reload bungeehelp.reload - Reloads the configuration.
bungeehelp.view - Allow the user to use help commands.
bungeehelp.cooldown.bypass - Allow use to bypass the command cooldown.
bungeehelp.updatenotify - Allow the users with this permission to get a message if a new version of the plugin is avaiable.
And don't forget to leave a review if you like the plugin. :)