A permission node is a string that usually contains multiple words separated by periods. These permission nodes are given to players to allow them special privileges on the server. An example of this is bukkit.command.give, which is the permission node that is needed to execute the give command. As you can see, it can be broken down into three parts, namely, the creator (Bukkit), the category (command), and the specific privilege, (the give command). You will find most permission nodes to be structured this way. For any plugin, its permission nodes begin with the name of the plugin. This helps prevent any collision of nodes. If two plugins use the same permission node then an admin cannot limit access to one node and not the other node. You will also find that many plugins' permission nodes are only two words long. This is done when the plugin does not have many permissions. Therefore there is no need for categories.
To help you understand permission nodes properly...