It's been a long time coming, but with the accomplishment of build 1000 Bukkit has finally accomplished a built-in Permissions system (codenamed Superperms). For more info on how they work, and how to integrate them with your plugin, see the official Permissions FAQ. Keep in mind that you should rarely, if ever, have to hook this plugin directly; instead keep things in the realm of checking player.hasPermission("yourplugin.node").
Click here to come to the commands.
Click here to come to the permissions.