pain is a sensational response to something physically happening to your body
the cause of the pain is usually a real thing, but the sensation is still just a sense....so technically it would still fall under genjutsu

and zabuza's mist would prolly be a ninjutsu, not genjutsu....since he was literally using chakra to turn the water into mist

as for the darkness jutsu, unless they actually showed the anbu guys acknowledge it being dark or something (cant really remember), i would assume that it was more of just something that only the hokage saw. Some genjutsu affect the whole environment, while others affect only the target's perception of the environment. It wouldnt make sense for the darkness jutsu to fall into the former of those two categories, since it would hinder the sight of the 1st, 2nd, and orochimaru as well.