There have been several versions of military commissions. The first was through an executive order. In Hamdan v. Rumsfeld, the Supreme Court declared them illegal, so the new Military Commissions Act came along and was passed by Congress. That is also being examined by the Supreme Court. The ruling is expected in June 2008 on the issue that the new iteration of the military commissions strips the detainees of their right to habeas corpus.
The current courts exist under the law in the U.S. From an international human rights perspective, they're still well short of international standards. But they are U.S. law for those who are not U.S. citizens, in that particular context, who have been classified as unlawful enemy combatants, and all that sort of thing.
On whether there's a single human rights organization that hasn't condemned the Khadr case, I don't know of every human rights organization in the world, so I couldn't say that definitively, but the big international ones like Amnesty International and Human Rights Watch have certainly expressed concern for years about this case--the detention of children in general in Guantanamo, and Guantanamo itself in connection with the whole war-on-terror detention system and the use of various techniques that violate human rights in that context.
On the third point, of whether there's been a serious investigation of his capture, we don't really know. I guess you're asking whether the U.S. administration has thoroughly investigated that or not. I'm not sure who you're asking, but access to that information is quite restricted, in the context of the military commission. On many levels we don't know. The information we have is what has been disclosed intentionally or accidentally to the media in the public sphere.