Is it permissible for someone to make a supplication to Allah to marry an already married, or an engaged woman?
No, it isn`t, and the person who does so is sinful before Allah, The Almighty.
Is Making up Missed Obligatory Prayers an Obligation?
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.
Missed obligatory prayer/prayers is a debt upon Muslim and making it up is an obligation, since the Prophet (PBUH) said: "pay the debt due to God, for it is the one which most deserves to be paid." [Agreed upon]. And Allah Knows Best.
Is it permissible for someone who has forgotten to mention the supplication pertaining to answering the call of nature to say it while in the toilet?
It is disliked for a Muslim to mention Allah while in the toilet, but he/she may recall the supplication in his/her head without uttering it; that is in case he/she had forgotten mentioning it before entering the toilet.
Is Zakah (obligatory charity) due on the money saved for marriage?
Zakah is due on the money saved for marriage if it reached the Nissab (minimum amount liable for Zakah), and a whole lunar year had lapsed over possessing it.