I'm not sure if it's the right place for this question but I have to ask. I've just made my way through the wiki and I have a problem. I don't know what permissions can be used for commands and world interactions. There are some of them at the wiki but many commands aren't mentioned there. Is there a list of possible permissions somewhere?

There is no full list -- every plugin defines its own permissions, so you have to look at the documentation for each plugin you use.

But there is one thing. What permissions does minecraft vanilla have?

Vanilla minecraft doesn't define any of its own permissions -- depending on which platform you're using either Bukkit or Sponge's documentation will list all the permissions that are used. You can always run /pex toggle debug (1.x) or /pex debug (2.x dev builds) to see which permissions are being checked when you try do do things and change settings based on that.

Thank you.

And what about all nodes that are directly within permissionsex?