Is it permissible for a woman to shake hands with her brother-in-law?

It is forbidden for the woman to shake hands with her brother-in-law because he isn`t a Mahram (unmarriageable) of hers.

Does passing wind from the anus affect ritual purity?

Ablution is nullified by the passing of wind from the anus, but washing the anus is not required as wind leaves no impurity.

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 (PBUH) 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 (PBUH) 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." [Agreed upon].

However, not all the deceased are in the same situation because Allah The Almighty Knows: "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..

Is it permissible for a woman who is in her confinement to fast upon seeing blood signs that are neither black, nor red ?

Brownish, reddish, and yellowish discharges are all considered confinement until there is no colored discharge which marks the end of confinement. Moreover, the aforesaid woman is prohibited from fasting until she attains ritual purity. And Allah Knows Best.