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.
Is it permissible for a Muslim physician to specialize in gynecology obstetrics, and what is the ruling on working as such?
Some fields of knowledge are an individual duty while others are a collective one, and specializing in gynecology obstetrics is a collective duty. However, if there were female physicians to treat women, then there is no need for a male gynecology obstetrics specialist to look at women`s Awrahs (private parts) except in necessary situations since the jurisprudential maxim says:” Necessity must only be assessed and answered proportionately.” And Allah Knows Best.
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.
A pious man proposed to me and my father was hesitant in this regard because he is black, am I sinful if I accepted his proposal?
If the suitor is pious, color isn`t a drawback. However, try talking to your father kindly, so that he approves of your marriage with contentment, and that is better for you.