I can vouch for both Fort Union and Pipestone. Pipestone has a wonderful tallgrass prairie with gorgeous flowers (even in September, which was the month I visited in 1999) as well as the chance to watch a Native American carver working on the eponymous stone. Fort Union was a fascinating example of an early trader's fort, and North Dakota's Fort Buford State Park, just down the road, was the corresponding military part of the story. Also, the reason for the location of both forts surprised me greatly -- I'd had no idea that the water that goes over Yellowstone Falls, and the water from Old Faithful, don't mix until they reach North Dakota. Quite amazing.

Another interesting often overlooked unit of the national park service (at least it seemed so to me when we visited there when I was a teenager, several decades ago) is Capitol Reef National Park. At least in comparison to all the other units in Utah. Someday I'm going to go back there...

Lake Mead NRA. I know that even in NPS circles it is viewed as “a piece of fish tank gravel among the crown jewels” while never having been there I am sure it has some good features. Besides, without Lake Mead where would all the gangs from Las Vegas hang out.

I love the small, obscure NPS units -- they've been some of my better park experiences.

I'm going to throw Hovenweep NM into the mix. The last two times I've visited, I've gone out to the outlying sites: Holly and Horseshoe/Hackberry the time before last, and the Cajon group last time. I still have Cutthroat Castle left to see for another visit. All these sites offer a great chance for some profoundly solitary experiences. But even if you only make it to the main Square Tower Group, it's still a great visit -- the Little Ruin Canyon Trail is a great hike, and the campground was one of the more surreal NPS camping experiences of my travels my last time there, as I had it all to myself that night (but the intrepid ranger still gave the evening program to his audience of 2 -- me, and the camp host!).

I also would note Tonto NM, Navajo NM, City of Rocks NRes, and any of the "Fossil" monuments (John Day, Florissant, Agate, Fossil Butte et al), as well as the ones mentioned above. I also really enjoyed some of the obscure sites I've visited back east, like Maggie Walker NHS, St Croix IHP, and Thomas Stone NHS.

But the ultimate overlooked site is the undeveloped Yucca House NM. Definitely interesting when I took the time to find it and visit a few years back. I hope it always stays as it is now -- an obscure little oddball in the NPS System!

I'll add Salem Maritime National Historic Site. Located in urban Salem, MA; people come to Salem to the witch-related attractions, a phenomenon that lasted just three months in 1692 and neglect Salem's storied maritime history. At one time Salem was the sixth largest city in America; a world-famous port that ranked with Boston, New York, Philadelphia, Baltimore and Charleston, SC; the richest city in America per-capita thanks to it lead in opening new areas of trade in distant lands, especially China and the East Indies. It includes historic houses, the three styles of colonial architecture, the Custom House in which Nathaniel Hawthorne worked and a recreation of an East Indiamen, the type of vessel used in the trade. The site is on the waterfront and all of these are open to the public - when and if visitors discover they exist!

Pipespring N.M. out of Fredonia Arizona. Only 40 acres, this important site preserves a water source critical for the Piutes for eons probably, taken and developed by early Mormons as a tithe property for the church. Teriffic preservation of important structures, nice little visitor's center, great place to bird. Big views.

As someone else commented, the NPS sites are great but I spend more time in undeveloped and underappreciated sites largely on BLM lands. More freedom to explore, camp, relax without the strict use policies of the NPS. Just sayin'.

Charles Pinckney National Historic Site just outside of Charleston - definitely.

But the rangers and volunteers at the site are so enthusiastic about.

I share MikeG's enthusiasm for Pipe Springs National Monument. It tells the story of the encounter between early Mormon pioneers and the Paiute Indians who had live there for generations.

Another site that intrigued me was Eugene O'Neill NHS in California. It is the only site in the System that I can think of that commemorates the contributions of an American playwright. It's hard to get to. When I visited, there was a shuttle bus into the site to satisfy neighbor's desire that not many private cars enter their neighborhood.

I like Booker T. Washington National Monument in southern Virgina. I was also fascinated by Minuteman Missle National National Historic Site in South Dakota. The best part of a visit there is to descend by elevator to the heavily-bunkered site where the "misslers" stood their shifts. The door to the cubicle is a huge swinging steel door to which some unknown soldier had pasted a Domino Pizza sign: "Your delivery is guaranteed in 40 minutes or the next one is free." This was a grim reminder of the Cold War.

Rick

Capitol Reef National Park is really out of the way, so it's not a place that you might "stumble upon" on the way to someplace else.

But it's a wonderful Park. The campground is in the middle of fruit orchards planted in an old Mormon settlement. There are some great canyon hikes there. It's surrounded by National Forest land.

Outside of the Park, there are several viewpoints where you can look across this huge "fold" in the earth's crust...very impressive.