Which is better, to pray at a prayer place (Musala) whereas many people pray in it, or at a near by mosque in which a few people perform prayer?
Praying at the mosque that has a bigger number is better so long as the number of praying people at the other mosque permits performing prayers in congregation. And Allah Knows Best.
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.
If a father stops his daughter from getting married, is it permissible for her to conclude the marriage contract herself?
It is permissible for the father to stop his daughter from getting married if there was a lawful reason for that, and she isn`t allowed to conclude the marriage contract without her guardian. However, if her father denied her right in getting married for an unlawful reason, then she should go to court.
What is the ruling on a person in a state of major impurity (junub) or a menstruating woman (ha'id) reciting the Quran from memory?
It is not permissible for a menstruating woman, a postpartum woman, or a person in a state of major impurity to recite anything from the Quran, whether from memory, from the Quran, from a phone, or a computer. It is also not permissible for them to touch the Quran, based on what was reported from Ali bin Abi Talib that the Prophet (peace be upon him) was not prevented from anything regarding the Quran except major impurity (janabah). (Reported by al-Tirmidhi who said it is a hasan sahih hadith). Menstruation and postpartum bleeding are analogous to major impurity (janabah) as they are all major impurities (hadath akbar).
For those mentioned, it is permissible to mention Allah and supplicate even with verses from the Quran, provided they do not intend them as recitation of the Quran, but intend them as remembrance (dhikr) or supplication (du'a). And Allah the Almighty knows best.