I dont know if this is already known or if i already said it, but iff you shoot like 7 missiles to mother brains eye and then shoot a super missile you can do more damage then only missiles.
Hard: I don't know, but probably 2 missiles, then Super Normal: 4 missiles, then Super Easy: 4 missiles, then 2 Supers I think. I'm not sure though: I don't have the game to hand. Presumably the theory is to do more damage than normal in the round by almost filling then firing a super to overfill the "round quota".
In normal it will finish the battle in 44% fewer rounds, or 80% more quickly. (meaning in 4 rounds). You need 16 missiles and 4 supers.
Normal: 5 missiles to shot, so 4 normals then a super or a super right when the previous shot goes out and then another super to get her to shoot. Hard: Same thing, only with 3 missiles per eye shot, so just shoot 2 then a super, or the other method mentioned above.