Is the marriage contract considered valid if concluded at home by the marriage official (Ma`zon)?
Yes, it is valid as long as it is registered at the court.
Is it permissible for the father to give the Zakat of his money to his poor married son?
It is permissible for the father to give part of the Zakat to his poor son, if the latter was sound and healthy, because in this case the father isn't obliged to spend on his young son, even though; he is considered one of the Muslims poor. And Allah Knows Best.
I am a doctor, and sometimes I refer patients to the hospital for surgical interventions, and they give me a commission from the fees of the surgeries, even though I do not perform these surgeries. What is the ruling?
All perfect praise be to Allah, The Lord of The Worlds, and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions.
If this commission is charged to the patient as part of the operation costs, then it is not permissible. Additionally, a doctor should only recommend surgery if there is a genuine medical need, and the hospital should only perform an operation when necessary. And Allah The Almighty Knows Best.
Does ill-gotten money hinder the answering of the Du`a (supplication) and the means of subsistence?
Sins hinder the answering of the Du`a, and deprive the sinner from means of subsistence; whereas, acts of obedience facilitate making a living. Allah, The Almighty, Says (What means) : "And for those who fear God, He (ever) prepares a way out. And He provides for him from (sources) he never could imagine." [At-Talaq/2-3].