Yes, students can pray at school if they want.

I don't know why it matters. As long as they do it in their head and not out loud it shouldn't bother anyone.

What bothers me is other people can wear turbans in school and i can't wear a regular ball cap. Whats the difference?

I don't think they should have to "do it in the head".  They should be able to do it aloud as long as the school administration/teachers do not encourage or require it.  It should be a personal choice regardless.

Now, if someone prays aloud that, "God kill the heathen", then that's not okay.  But if someone were to pray to Allah and ask for guidance, or blessings, there is no problem to be reckoned with here.

I dont agree with any kind of censorship, if a guy wants to sing religous songs let him who cares, just go away if u dont like it.
I go to a catholic school, I dont know how are things in public schools in my country, but in the morning teachers pray. They often get annoyed because we laugh or play with cell phones/DS/PSP but there are some classmates that pray.

School prayer is acceptable so long as it passes the "endorsement test" which is simply a section of the "lemon test." If the prayer in question appears to be endorsed by the school, then it violates the establishment clause. This was the case in "Santa Fe Independent School District v. Doe." In SFISD v. Doe, the SC ruled that student led prayers before a football game violated the establishment clause because they were delivered over the school's public address system. If students desire to pray by themselves in a classroom or before a football game, that does not violate the establishment clause.

Thanks for the reply. Now, couldn't someone say that if students wanted to pray together in a classroom, that they are doing in the property of the school and that would be the school endorsing something religious?

So, where is the line drawn?

Like the case of the girl with the song Amazing grace. Is that too far?

"Lead prayers" is different from "pray by themselves", there is the line.

Well, i don't know about the situation on the U.S, but where i live, most schools endorse a religious tolerant attitude, but are clearly in line with a more christian line of thought and religion.
I grew up on a heavily based christian family and education, and although now i'm wicca, i have a lot of respect for every kind of religion, i think each one has something different and unique to teach us.

The students can do whatever they want religiously, the school can have no part in it. Praying in a classroom is fine, a group of students praying in a class room is fine, a teacher asking kids to pray in the class room:wrong, the principle giving permission to use the school intercom to pray outloud to the entire school:wrong, players praying before a game in a huddle is fine, coach telling the players to get together and pray: wrong.

The case with the girl and amazing grace I doubt was law, so much as that school's personal decision. And whether you agree with the reasoning ethically, they do have the right to veto what goes on in their school talent show. They aren't required to let somebody sing a song just because it's religious in nature and have to respect that, if they feel that it could be offensive to the rest of the student/teacher body. But their decision on the matter isn't a law.

The pertinent question broached by the "endorsement clause" is: would a reasonable obeserver perceive that the government (school) is approving or disapproving of the message? I imagine a reasonable observer would perceive students praying in a classroom as neither the approval nor disapproval by the government (school). Also, the SC ruled in Tinker v. Des Moines ICSD that 1st Amendment rights apply to public schools. This means that the government (school) can neither endorse an establishment of religion nor prohibit the free exercise thereof. I am not familiar with the case of the girl being prohibited from singing "Amazing Grace." That could go either way, in my opinion.