Jeremy, like you I did put in my ten hours watching Ken Burns documentary: THE WAR. Every time that I drive past Manzanar (WW II Japanese Detention Center) which is settled on the east side of the Sierra's, it's hard to imagine the extreme hardship that this nation went though during WW II...and it's Japanese citizens. Manazana is located with a beautiful backdrop of the majestic Sierra mountains, yet it composes a stark nakedness and loneiness for which it's location sets. My deceased uncle served in the United States Marines as a combat soldier and saw some of the bloodiest war campaigns in the South Pacific. His war trophies were settled by the fireplace mantle inside his quaint Iowa farm house: a cup of golden teeth extracted from dead Japanese soldiers. His hearing was severly impaired from the concussions of heavy artillery gun fire, but he never spoke a word about "The War" to me or about his war injuries. His pain of the war was greatly relieved by being a gentle productive farmer back in Iowa...which he was better at that then killing.

And don't forget the Ahwahnee in Yosemite was transformed into a military hospital for recovering vets during much of the war. There are some amazing photos in the Yosemite Research Library of the tents set up on the Ahwahnee lawns.

There must be a story for many, many parks in the system. Fort Jefferson (Dry Tortugas) was a seaplane base during the war and they cut down trees in the Everglades to make up for a shortage of wood for houses.

If you are in Boston the Charlestown Naval Shipyard National Park is home to the U.S.S. Cassin Young which is a WWII built destroyer. She is currently in her 1950's configuration, but she was hit by two kamikazes. The last one just two weeks before the war ended and potentially the last ship hit by a kamikaze in the Okinawa campaign. Even in the 1950's condition she retains most of her WWII equipment and looks. She is in good condition and free of charge. She is located across the pier from the U.S.S. Constitution. Two great ships one worthwhile visit.

At Fort Sumter in Charleston, SC, the USS Yorktown(the 2nd one) is open to tour. I don't remember it actually being a NPS site but you pay to enter at the same place you pay to tour Fort Sumter. I spent 7 hours on it and didn't want to leave. I missed seeing Fort Sumter!
In Fredericksburg, TX near LBJ Ranch, there is the George Bush WW II Museum & Nimitz Museum. It's my favorite museum in the world. Once again not really an NPS site but associated close enough to be mentioned.

In the Fremont National Forest in Oregon, there's a monument to Elsie Mitchell and five school children. They were killed instantly in 1945 when a Japanese balloon bomb exploded. The Japanese built these bombs and set them aloft in the jet stream to drop on the United States. The goal was to cause mayhem, terror and forest fires. These bombs fortunately mostly exploded harmlessly or didn't explode at all except for the tragic case in Oregon. These children and Mrs. Mitchell were the only casualties on the U. S. mainland from enemy action during World War II.

Jeremy,
There are a lot of war monuments and memorials that are not in the US Park system. I have been to the two Pacific arena national cemetaries that include memeorials. One is in Honolulu the other is in Manila. Both are very inspiring and a tremendous tribute to the men and women who are buried there.
Here is the url to the American Battle Monument Commision; http://www.abmc.gov/home.php It includes information for other wars as well.
Best regards