Is it permissible for someone to make a supplication to Allah to marry an already married, or an engaged woman?
No, it isn`t, and the person who does so is sinful before Allah, The Almighty.
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.
I am an author, and I have books stored with me. Is it permissible to pay my zakat in the form of books containing beneficial knowledge for poor students, such as chemistry and mathematics, or religious books that spread Islamic sciences?
Zakat on wealth must be paid in cash from the wealth itself. Therefore, you should pay your zakat in monetary form so that the poor can purchase what they need. And Allah Knows Best.
What should a person, who delayed making up missed fasts of last Ramadan due to the continuance of the same excuse, do?
It is permissible for one, whose excuse for not making up missed fasts of last Ramadhaan has continued, to delay fasting until the excuse ceases to exist, and he is considered neither sinful, nor obligated to pay a ransom. And Allah Knows Best.