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.
Is it permissible for a woman to use a contraceptive without telling her husband although he wants to have as many children as possible and she can`t care for them?
All perfect praise be to Allah, the Lord of the Worlds, may His Blessings and Peace be upon our Prophet Mohammad and upon all his family and companions.
If the pregnancy is harmful to the woman, it is permissible for her to use a contraceptive; however, this has to be backed by a medical report from a God-fearing doctor. In addition, you had better inform your of what you are doing to avoid dispute. And Allah The Almighty Knows Best.
What husband's stand should be, if his wife disagrees with his mother?
Both the mother and the wife have rights on you (Questioner); therefore, you are obliged to treat both justly, resort to wisdom to please both and intiate reestablishing cordial relations among them. And Allah Knows Best.