In the February 13 & 20, 2006, issue of "The New Yorker," Hendrik Hertzberg touched on an issue that has bothered me since the days immediately after the events of September 11, 2001:
"In calling it a war, Bush emphasized its seriousness, but at the cost of granting its criminal perpetrators the dignity of warriors."
The metaphor of "war" has many problems, but what I immediately disliked about the phrase "war on terror" back in 2001 was that it seemed to eliminate the possibility of dealing with Al Qaeda as a criminal organization whose members should be put on trial in criminal courts. That dislike has been more than justified: the United States has put almost no-one on criminal trial for the September 11 events (or if it has, it has declared the results secret and hence eliminated any public effect that such trials might have, if only for the morale of Americans). In contrast, just to name two other countries, Spain has had criminal trials about the Madrid bombings, and Italy is also pressing criminal charges against "the self-proclaimed mastermind of the Madrid bombings."
I mentioned the problem of "war" as the central metaphor to an acquaintance in October, 2001. She happened to have once been George H.W. Bush's personal assistant (after he was no longer President). She said that starting a war against Afghanistan did not preclude judicial approaches to September 11. Unfortunately, it has.