Is it permissible for the children of a deceased father to settle his debt from the Zakah(obligatory charity) money due on them?

It is impermissible to use the Zakah of one`s money for settling the debts of the deceased. However, children should settle the debts of their deceased parents out of filial piety.

Is it incumbent on a husband to pay the alimony of his wife if she had left him and stayed at her parent`s without his permission?

When a wife leaves her house, and stays at her parent`s without asking her husband, she is considered a Nashiz(wife who refuses to abide by her husband’s orders), and so she doesn`t deserve an alimony.

What is the ruling on staring at the Holy Ka'abah?

Staring/looking at the Holy Ka'abah is an act of worship even if this took place while performing a prayer, since Al-Baihaqee stated that the Prophet (PBUH) said: " Staring at the Holy Ka'abah is an act of devotion." [Sho'aab Al-Imaan]. And Allah Knows Best.

Does the deceased hear the supplications or recitations of those visiting his/her grave? And does making constant supplications for the deceased who didn`t adhere to performing the prescribed prayers ameliorate his/her affliction?

Praise be to Allah the Lord of the Worlds.

In principle, the dead hear the living since it has been rigorously authenticated that the Prophet (peace and blessings be upon him) ordered the bodies of the idolaters slain in the Battle of Badr to be buried. He then approached them and called them one by one and said, “Have you found what your Lord promised to be true for we have found what our Lord promised us to be true.” ‘Umar asked him, “O messenger of God! Why do you speak to lifeless bodies?” The Prophet (peace and blessings be upon him) replied, “By the One Who has sent me with the truth! You do not hear my words better than they do except that they cannot respond.”{Related by Bukhari & Muslim}.

However, not all the deceased are in the same situation because Allah the Almighty says, "Before them is a Partition till the Day they are raised up."{Al-Mu`minun, 100}. Moreover, supplication reaches the deceased. And Allah knows best.