Is it permissible to have prisoners of war, and should they be prosecuted, if so then how?
In the beginning, it's not allowed to have prisoners of war until the enemy has been thoroughly subdued =
"It is not for a prophet to have prisoners of war until he has thoroughly subdued the land." [8:67]
Once the subjugation has been accomplished, only then are we allowed to have prisoners =
"If you meet in battle those who disbelieve, smite their necks. Then, if you have thoroughly subdued them, the bind them firmly, so there will be a time for either generosity or ransom for them until cessation of the war." [47:4]
After someone is taken as a prisoner, they have many rights in Islam.
They aren't allowed to be forced to become Muslim and have the right to remain on their own religion =
"O Prophet! Say to those who are captives in your hands: 'If Allah finds any good in your hearts, He will give you something better than what has been taken from you and He will forgive you. For Allah is Oft Forgiving, Most Merciful." [8:70]
You can read how the Prophet treated a prisoner named Thomamah bin Athal and he became Muslim because of the kindness he was given even though he fought against the Prophet.
A prisoner has the right to be fed =
"And they give food in spite of love for it to the needy, the orphan, and the captive, [Saying], "We feed you only for the countenance of Allah . We wish not from you reward or gratitude. Indeed, We fear from our Lord a Day austere and distressful." [76:8-10]
A prisoner has the right to be clothed if naked. Al-Abbas was captured as a prisoner and was undressed. The Prophet gave him a shirt to wear. You can read about it here
What else is there?