Over at E-splatter.com, Lucius Gore selects the Top 10 Horror Movies Inspired by the Iraq War. The list contains obvious titles like LAND OF THE DEAD and 28 WEEKS LATER, plus some less obvious ones like THE MIST and THE SIGNAL
Although neither are horror films, I would add CHILDREN OF MEN and REDACTED to the list. The later, particularly, although not a great film, takes an unflinching look at the war in a horrifying way that makes the fictionalized horrors pale in comparison.
The E-splatter list includes THE HILLS HAVE EYES, because it is more highly regarded than its sequel, but THE HILLS HAVE EYES II actually makes the Iraq connection more explicitly, with a group of soldiers on a training mission in the American desert who run afoul of mutant cannibals.
I would also mention THE TEXAS CHAINSAW MASSACRE: THE BEGINNING. Although it is set during the Vietnam war, I think it safe to say that it is referencing the Iraq War, in the same way that M*A*S*H used the Korean War as a stand in for Vietnam.