We do it to our own soldiers, regularly, as a means of preparing them to cope with capture and being tortured.
It isn't in the same category as slicing off body parts or prying off fingernails.
Having said that... these militia people that have been arrested are American citizens, whatever they are accused of. If they have no rights, then I have no rights and you have no rights.
If you catch a foreign national planting a roadside bomb in Iraq for an American convoy, waterboard that sucker. If you catch a foreign national in America with evidence he is part of a major terrorist plot, waterboard that sucker.
We shouldn't be doing it to our own citizens however. There's this little thing called the Constitution.
Yes, I make the distinction between Americans (not waterboard-able due to BoR) and not-Americans found to be involved in terrorism (waterboard-able). Perhaps you think this is an unequable viewpoint. I don't care. If you're an American you are my countryman and protected by the Bill of Rights. If you're a foreigner known to be plotting terrorism against my country, screw you.