I dont exactly know what you are talking about. Try to be more specific. I am not really sure what you are talking about, but I think you should check out the server.properties file and the bukkit.yml file.
He means like what would the permission note for the command /gamemode Jasonsj10 1 Like i would say bukkit.gamemode (I know that isnt it, Just a example)
I don't think there are any . I know that a plugin called DefaultPermissions which will give vanilla commands and bukkit commands to people through Permissions, however it is unofficially inactive. This means that they new 1.8 commands will probably not be added to it and you will be forced to move the (superior) SuperPerms system which has these nodes built into it.
Not all. I have a lot of plugins and I am starting to notice that plugins are starting to use superperms
I think he was referring to the fact that Permissions still works with Bukkit, however you are completely right that most new plugins don't support it and some plugins have updated and no longer support it.
the gamemode command doesn't really have a permissions node atm. If a plugin figures out how to call this, and then parse it out via a perms node...i haven't heard of it.
I did a permissions dump on myself (as an op), and bukkit.command.gamemode looks like the gamemode node you were thinking of ^^.
