Essentials has a feature that will limit the plugins commands in help by permissions, this however requires a little work on behalf of other plugin authors.
Take this GroupManager plugin.yml example:
manuadd: description: Move a player to desired group.(Adds to the file if not exists) usage: /<command> <player> <group> permission: groupmanager.manuadd
You will notice that there is a new node "permission". This should relate to the permission required for this command and if this node is present essentials will look for it and limit help accordingly.
The one downside to using 'permission' is that bukkit uses this convention as well, and will do a permissions check prior to running the command. If you want to do your own permissions checks, and not rely on bukkit, use 'permissions:' instead.
If you like the sound of this, please ask politely for other authors to add this new node in their plugin.yml under their commands. We will be happy to help them with any issues regarding this.