Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Is it obligatory for a wife who has been abandoned for many years to observe the waiting period (iddah) after her husband passes away?
If her husband passes away, the wife is required to observe the waiting period (Iddah), even if he had abandoned her, because she is his wife and inherits from him, so she must observe the iddah after his death. And Allah Knows Best.
My father placed shares worth twenty dinars in one of the banks, and their value doubled to become five thousand dinars. When my father passed away, one of the scholars told us that it is permissible for us to take the money. What is the ruling on this money, considering that it comes from a bank and involves interest (Riba)?
Allah The Almighty Said (What means): "And if you repent, then for you is the principal of your wealth. You do not wrong, nor are you wronged." [Al-Baqarah/279]. This is the precautionary ruling regarding what you are asking about. You are entitled to the principal amount, and you should give the excess as charity to the poor and needy. If you are poor, you may take from it. And Allah The Almighty Knows Best.
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.