I believe that it is ok if an individual wants to pray at a school just to him/herself praying and minding their own business; however, a formal school prayer should be banned because it is just not right for the minority religions at the school if they are forced to say any prayer that has no relevance to them, we have to allow everyone freedom, what next an Islamic or scientology or Jewish prayer, will our students just go to school to pray; however, if an individual wishes to pray on their own time they have a constitutional right to do so- don't forget the Atheist, we have to be equal and practical if we plan on keeping America a place of liberty and freedom, that is the first part of the bill of rights
I do not disagree that students should be allowed to pray in schools. That would be a prohibition of religion and not right according to the US Constitution (I am assuming we are talking about the US, but this applies in any country that has freedom of religion). But a formal school prayer (accompanying the Pledge of Allegiance in the morning or something similar) should be prohibited, as that would be discriminating to all that are of a different religion than the one according to which the prayer is held, and all that have no religion (Atheists, like myself). Even the opportunity to opt out is not really an opportunity, especially (but not only) in certain places like many southern states in the US, where the minority (whether of no religion or of another religion) would likely be excluded socially because of their faith or lack thereof, and might even be bullied because of that. Also, a prayer that gives people the opportunity to opt out is still not feasible in accordance with freedom of religion, as it would prefer one religion over another. Therefore I am against formal prayer in school.
Formal school prayer, which I am assuming refers to a single prayer in the morning observed in all classrooms, seems like freedom of speech. But formalizing it isn't freedom of speech, it's restriction to those who choose not to participate. No one is advocating that the ten Christian or Muslim or Jewish kids in the room can't be allowed a reasonable amount of time to complete the prayers their subset requires or deems compulsory to the religion, but to ask all students to stand for THE prayer "but you may choose to opt out if you wish" only creates contempt and division between students that isn't necessary.
This also implies a very dangerous idea to children who are not mature enough to differentiate, which is that prayer is something everyone does on a daily basis and is therefore socially respectable or even required to conform to normal standards and be accepted by peers. Reality shows that in fact only 51.9% of Americans identify themselves as Protestant Christian(http://www.Gallup.Com/poll/159548/identify-christian.Aspx). To give children the idea that Christianity, or even a religious viewpoint is so normal that it's taught in school is unfair to the world they will meet upon reaching adulthood.
Further, there is no such thing as a nondenominational prayer. If we were to sanction a so-called "non-denominational prayer" what would it say? Catholics believe good works are required to enter the kingdom of heaven, while protestants require only repentance (grace). Muslims generally believe that Mohammad was the Lord's prophet, shall we include Christ as a lesser prophet as he is in the Koran, or must he be referred to as the son of God(in Jesus name we pray, amen)? Judaism is still waiting for the Messiah, do we cut Jesus out for their sake?
When people want school prayer, what they are really saying is that they want a Christian prayer, and who cares about the social repercussions of sitting out, because you're going to hell anyway.
The United States is primarily made of Christian beliefs. Therefore, prayer should be allowed in schools. "Under God" should remain in the pledge which should still be said every morning. Those who are non-believers should not be forced to cooperate. It would also be reasonable to have separate prayer classes or clubs for those that want to participate. I'm a fan of the saying, "As long as there are tests there will be prayer in schools."
The issue of prayer in public schools should be up to each school district, not Congress. The reason is that there should be the freedom of any and all religious beliefs to have prayer time before and after school on school property. If Christians want to pray, then so should Muslims, Hindus, Sikhs, Jews, Buddhists and even Satanists. Prayer isn't illegal--preferring one religion over another is.
When it comes to prayer in schools, there is absolutely no doubt in my mind that school organizations and their employees should not be allowed to organize such events. However, students should be free to exercise their own religious freedom and arrange formal prayer sessions outside of class time on school campus. If intimidation or bullying become a problem because of this, either by or against the prayer organizers, then faculty should get involved.