I prayed all the obligatory prayers in congregation, but after finishing the `Isha prayer, I remembered that I had forgotten to pray Dhuhr. What should I do, and is my prayer invalid?
Your prayers are valid, but you must make up the Dhuhr prayer as soon as you remember it, based on the saying of the Prophet (peace be upon him): "Whoever forgets a prayer must pray it as soon as they remember it; there is no expiation for it except this." [Muslim]. And Allah knows best
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.
How should I be kind to my atheist father?
Allah, The Exalted, has decreed and ordained his slaves to be kind with parents, even if they are polytheists, by honoring and obeying them in all that isn`t sinful, so that they might love Islam and embrace it as a result.
Is it permissible for a praying person to make supplication in each Sajdah (a prostration) of obligatory prayer?
It is permissible for a praying person, whether praying individually, or in congregation, to make supplication during Sujood (prostration) in obligatory, or voluntary prayers. However, it is disliked for the Imam to do so since he is required to spare the prayer performers any sort of hardship, unless he is leading a certain group who don`t mind him extending the prayer.