I was thinking about this because of the International Criminal Court, as people complain that the ICC gives fewer protections to the accused than the US Bill of Rights does.

Superficially, "If you meet in battle those who disbelieve, smite their necks" in a religious text tends to be interpreted as meaning those who disbelieve religiously.
But the explanation of the first article seems to be that it really means those who disbelieve reality, i.e. those who refuse to admit that they have been taken prisoner and must now submit in body (but not in mind or spirit) to the enemy.

Moreover, my skimming of the articles gave me the impression that Islamic law deals only in war between Muslims and non-Muslims; that war between people of the same religion was not thought possible.

I am also curious as to whether Islamic law could justify the same kind of "switch" that the US government is pulling on the "enemy combatants" at Gitmo, pretending that they are not POWs and thus unprotected by Geneva.

"According to Muslim law, a prisoner qua prisoner cannot be killed. Ibn Rushd even records a consensus of the Companions of the Prophet to the same effect. This does not preclude the trial and punishment of prisoners for crimes beyond the rights of belligerency. For this, we possess the high authority of the practice of the Prophet when two prisoners of the Battle of Badr were beheaded by his order."

But if the prisoner is a soldier in an illegal and illegitimate war, is he really a prisoner? Certainly America's own failure to be clear and honest about its prisoners' status would make a similar vagueness by Iraq understandable.

If a Muslim country has entered into an agreement, it is bound by the terms of that agreement for as long as it is a party. There is complete consensus of the scholars on this issue because the Quran is very clear that contracts must be upheld. The Muslim country is free to give more rights and protections than the treaty or agreement calls for but must not give less. If Islamic law gives more rights and protections then it is hard to imagine under what justification a sincere Muslim could fail to uphold those rights and protections. It would seem more likely that there would be a problem if Islamic law gave fewer protections. If the Muslim country did not plan to go beyond what Islamic law called for, it should not enter into any agreements that go beyond it.

Regarding war between two groups of Muslims, there is in fact justification for this if one of the groups is doing wrong. This is discussed briefly in my article Muslims, Stand Up for Justice. However, you're correct that it isn't discussed much. As far as I know, the same rules would apply.

Finally, regarding the "switch" arguments applied by the U.S. I am not aware of any justification that could be made under Islamic law for this. I am not very knowledgeable in this field, so I hesitate to say too much, but from what I have read Islamic law simply distinguishes between combatants and non-combatants and the definition of a combatant is someone who takes up arms to fight. Another thing I do know is that if a Muslim soldier in the course of battle comes upon a person who offers peace, he has to accept that offer of peace. O you, those who have faith, when you go out to fight in the path of God, make things clear and do not say to someone who gives you peace, "You are not a believer," - you coveting the pleasures of the life of the world, and with God is abundant reward. You were the same as that before, then God was gracious to you. So make it clear. Surely God is aware of what you do. - Surah an-Nisa verse 94.

A Guide to the Perplexed about the Permissibility of Killing Prisoners"
In an article titled "A Guide to the Perplexed Regarding the Permissibility of Killing Prisoners," which appeared in the column "Jihad News from the Land of the Caucasus[1] " the author suggests that the Islamic religious scholars present five different alternatives, drawn from the various interpretations of the Koran:
1. A polytheist prisoner must be killed. No amnesty may be granted to him, nor can he be ransomed.
2. All infidel polytheists and the People of the Book (i.e., Jews and Christians) are to be killed. They may not be granted amnesty, nor can they be ransomed.
3. Amnesty and ransom are the only two ways to deal with prisoners.
4. Amnesty and ransom are possible only after the killing of a large number of prisoners.
5. The Imam, or someone acting on his behalf, can choose between killing, amnesty, ransom or enslaving the prisoner.
Killing a Prisoner for the Sins of Others is Permissible
The last position is the one preferred by the author who explained that the Prophet Muhammad had dealt with the prisoners in different ways to maximize the benefits to Muslims.
He gives examples regarding the methods that the Prophet Muhammad had chosen to kill, grant amnesty, or ransom prisoners.
The author finds it necessary to present the subject in reaction to an Islamic criticism "which had torn his heart" about the execution of nine [Russian] prisoners after the Russian Government had refused to surrender "one of Russia's biggest criminals and crooks."
According to the author, [the Chechens] have executed the prisoners not because of their heart's desire, but because they have seen a benefit for the Muslims in such an act.
In reaction to the arguments made by some critics that no one should be punished for the sins of others, the author maintains that Allah permits the killing of a prisoner because he is a prisoner, and all the more so if his killing for the sins of others serves an important Islamic interest, as well as a deterrent (to the enemy). He brings examples from actions of the Prophet. A state of war justifies actions of the sort that could guarantee the security of the soldiers of Islam. Moreover, only with such action is it possible to protect the honor of Muslims.[2]
In an article titled "Are Hostages Prisoners?" the author explains the concept of "hostages" in its modern application to local kidnapped individuals and foreigners who are held as a means of pressure to achieve specific goals. According to him, he who was kidnapped in accordance with Islamic law should be considered a hostage, and hence a prisoner, who should be treated in the manner that would bring benefits to the Muslims.[3]

[1] In an article titled "Prisoners in Islam" the author indicates that there are five methods that Islam proposes for dealing with prisoners: release without ransom, ransom, killing, enslavement or subjugation to the authority of the Islamic state. The method changes according to circumstances but it has to be one that brings the greatest benefits to Muslims. For example, if amongst the prisoners there is someone who is strong and is likely to tantalize the Muslims and his keeping alive may cause harm to them, his killing will be the preferred method. If there is someone who is weak but wealthy, ransoming him is the best method. If there is someone who holds a favorable view of Muslims and could help them and their prisoners, amnesty is the best method. If there are those who could render a service, such as women and children, enslavement is the best method.
http://www.qoqaz.com/qoqaz.asp?9=4&pp=1&sec=7
[2] www.qoqaz.com/qoqaz.asp?p=4
[3] www.qoqaz.com/qoqaz.asp?p=4&pp=1&sec=8

I have cited the textual sources on Islam that I believe to be the most correct. The material you have posted is taken from a militant extremist site, as I am sure you well know. I have spoken over and over again about how these militant and extremist groups pervert Islam to justify their own actions. I'm not going to say it again.

I've also told you many, many times. I do not have control over any person other than myself. I can't answer for them or change what they do, I can only speak out for the truth as I see it. No matter how many times you ask me why some Muslims are wrong-doers my answer is always going to be the same.

I hope that someday we will be able to get beyond this impasse that we've reached and that you will be willing to look for the positive as well as the negative in Islam.