The statute applies not only to those who carry out the acts, but also to those who order it, know about it, or fail to take steps to stop it. The statute applies to everyone, no matter how high and mighty.
18 U.S.C. § 2441 has no statute of limitations, which means that a war crimes complaint can be filed at any time.
The penalty may be life imprisonment or -- if a single prisoner dies due to torture -- death. Given that there are numerous, documented cases of prisoners being tortured to death by U.S. soldiers in both Iraq and Afghanistan (see for example this report), that means that the death penalty would be appropriate for anyone found guilty of carrying out, ordering, or sanctioning such conduct.
You probably assume that this wouldn't really apply to the big boys running the country. But you'd be wrong.
Legal scholars have concluded that even the big enchiladas can be held guilty of war crimes (and see this).
The general in charge of the notorious Abu Ghraib prison in Iraq stated this week that Secretary of Defense Donald Rumsfeld and other top administration officials ORDERED that inhuman treatment and torture be conducted as part of a deliberate strategy. This confirms what the Pullitzer prize-winning reporter who uncovered the Iraq prison torture scandal and the Mai Lai massacre in Vietnam previously wrote.
The former director of the CIA accused Cheney of overseeing torture policies. Colin Powell's former chief of staff stated that Dick Cheney is guilty of war crimes. Some of the torturers themselves have come forward to confess their actions (see also this article; see also this article, this one, and finally this one).
Indeed, an FBI email declassified in December 2004 states that Bush signed an Executive Order authorizing torture (here is the list of documents obtained through a freedom of information act request, and take a close look, for example, at this one, which mentions the "executive order").
We now know that torture in Iraq was ordered by top officials, notwithstanding the administration's claims that it was only "a couple of bad apples" that were responsible for Abu Ghraib. Making a potential prosecutor's job easier, U.S. Attorney General Alberto Gonzales wrote a memo in January 2002 to President Bush saying that America should opt out of the Geneva Convention because top officials have to worry about prosecutions under 18 U.S.C. § 2441. By attempting to sidestep the Geneva Convention, Gonzales created a document trail that can be used to prove that top administration officials knowingly created a policy of torturing prisoners, and that such a policy could reasonably have been expected to result in the death of some prisoners.
The U.S. did opt out of the Geneva Convention for the Afghanistan war, but we never opted out of the Geneva Convention for Iraq. Indeed, President Bush has repeatedly stated that Geneva applies in Iraq (although he has since claimed that foreign fighters captured in Iraq are not covered). Thus, there would be very little room for fancy footwork by defense lawyers in a prosecution against top officials concerning torture in Iraq.
And to the extent that claims that the U.S. has sent prisoners to other countries for the express purpose of being tortured are true, violation of the war crimes act by the highest officials of our country would be even clearer. For who else but Bush, Cheney, Rumsfeld and other top officials would have the ability to authorize such flights? How could such a program be undertaken without their knowledge? And how could such a program be anything but the intentional "ordering" of torture, or at least "knowing about it" and "failing to take steps to stop it"?
It has recently come out that the leaders of the House and Senate Intelligence Committees knew about the torture occurring in Iraq, and about videotapes of such torture. At the very least, Senators Rockefeller, Roberts, and probably Graham and Shelby -- the two highest-ranking Senators on the Senate Intelligence Committee in the 107th and 108th Congress -- would have known. At the very least, Pelosi, Harman and Goss would have known.
Remember, it is a violation of the War Crimes Act of 1996 to even know about torture or to fail to take steps to stop it. The congressional intelligence committee leadership knew about the torture and they took no steps to stop it.