What is the ruling on reciting verses from the Qur'an over water, drinking it, and using it to break magic spells, heal illnesses, or burn jinn?
There is no harm on reciting verses of the Holy Qur'an over water and use it for cure. And Allah Knows Best.
Is it permissible to add the nutmeg to one`s food?
All Perfect Praise is due to Allah, The Lord of The Worlds
Using a little bit of the nutmeg for seasoning is permissible, but using a great deal of it is impermissible since it could lead to intoxication, and Islam has forbidden all intoxicants and stupefacients. And Allah Knows Best.
I took a car from the Orphans' Fund Development Institution; is there usury (Riba) involved in this transaction?
If the Sharia's conditions were met, then there is no harm in this. And Allah The Exalted Knows Best.
Is it permissible for the guardian, or the father of the child to hit the latter in order to teach him/her good manners?
It is permissible for the guardian to hit his/her child for teaching them good manners once they become ten years old provided that it is done mildly, harmlessly and without intimidation. Actually, such punishment is to be employed gradually i.e. after: asking, warning, and scolding. As for the teacher, he isn`t allowed to hit the student unless the latter`s father approves of it, and it is done according to necessity without intimidation, or harm.