Is it permissible for one to shake hands with his uncle`s daughter?
No, it isn`t because he is a non-Mahram (Marriageable) to her.
Is it allowed for me to donate a flat to each of my children except one considering that the tuition fees I paid for the latter`s university study are equal to the price of the flat? In other words, he has received his share and this is why I`m donating a flat to my other children?
All perfect praise be to Allah the Lord of the Worlds. May Allah`s peace and blessings be upon our Prophet Mohammad and upon all his family and companions.
Yes, it is permissible because you want to treat them justly. And Allah The Almighty Knows Best.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
A person is sponsoring an orphan and pays the sponsorship monthly. Is it permissible to pay this month's sponsorship from zakat money?
It is permissible to pay the orphan's sponsorship from zakat money if the orphan is poor and has no one to support them. The person must intend to count it as part of their zakat when paying the money. And Allah Knows Best.