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 it permissible to donate corneas to Jordan Eye Bank or all the organs via telephone?

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.

Corneas donation that is carried out after one's death is permissible by the Board of Iftaa'. Because this procedure is highly sensitive, the donation process

should undergoes to an accredited mechanism. And Allah, The Exalted, Knows Best  

Is it permissible for a woman whose menses exceeded (15) days to pray, fast and do what was prohibited on her to do during the latter period?

If the menses exceeded 15 days then it is deemed menstruation, and in this case she is obliged to pray and fast and to do what was impermissible for her to do during the latter period. In addition, she is obliged to make an ablution for each obligatory prayer after it's due time and making sure that impuity is removed. Finally, your menstruation period is over (Questioner) simlar to your menstruation in the previos month.

During a flight from Amman to the UAE, while we were flying over Saudi Arabia, the captain announced that it was time to break our fast, coinciding with the exact time of sunset. After I had broken my fast with my first date, the captain apologized for the earlier announcement and clarified that the correct time would be in 20 minutes. Am I required to continue fasting on that day?

Whosoever break his fast at teh very first announcement to make up the missed day of Ramadan, since Allah, The Most Exalted, Said (What means): "then complete your fast Till the night appears" [Al-Baqara/187]. And Allah Knows Best.