I know, I know: the title says "National Park Service Sites in Colorado" but I included a number of other sites from other agencies and even one Native American tribe in the list below. What to say? There's a lot to look at and I wanted to be sure nothing was overlooked...

Name, Location Acreage Comments
Alamosa National Wildlife Refuge
Alamosa, CO
Rio Grande marshland, migratory waterfowl, wintering bald eagles, self-guided tours
Anasazi Heritage Center
Dolores, CO

Beautiful museum displaying Anasazi artifacts and history. 2 excavated pueblos on site.
Arapaho National Wildlife Refuge
Walden, CO
Nesting and rearing habitat for migratory waterfowl, interpretive trails, self-guided tours.
Bents Old Fort National Historic Site
La Junta, CO

1833 trading post and Santa Fe Trail depot reconstructed.
Black Canyon of the Gunnison National Park
Montrose, CO
Spectacular canyon, viewpoints, interpretive exhibits, guided tours, includes 11,180 acre wilderness.
Browns Park National Wildlife Refuge
Maybell, CO
Prime wetland bottoms of the Green River in a semiarid region. Waterfowl, mule deer, pronghorns
Canyons of the Ancients National Monument
Visitor Center at Anasazi Heritage Center, Dolorado, Colorado
  Lowry Pueblo, Hovenweep National Monument in Colorado
Colorado National Monument
Fruita, CO
High plateaus, colorful canyons, wildlife, Rim Rock Drive, Tours.
Comanche National Grassland
Springfield, CO
Prehistoric cave art, dry shortgrass prairie, desert wildlife, 200 bird species, Lesser Prairie Chicken Natural Area.
Curecanti National Recreation Area
Gunnison, CO
3 large lakes created by dams along the Gunnison River in a volcanic landscape: Black Canyon and Curecanti Needle.
Dinosaur National Monument
Dinosaur, CO
Canyons, peaks, mesas, Gates of Lodore, Echo Park Road, riverboating, rafting, tours.
Florissant Fossil Beds National Monument
Florissant, CO
Interpretive exhibits, guided tours of an area with 80,000 plant and animal specimens fossilized over 30 million years ago.
Great Sand Dunes National Park & Preserve
Mosca, CO

The tallest sand dunes in North America at the foot of the Sangre de Cristo Mountains in the San Luis Valley
Hotchkiss National Fish Hatchery
Hotchkiss, CO
This hatchery produces 1.2 million trout annually for southwestern Colorado reservoirs.
Leadville National Fish Hatchery
6 m. SW of Leadville, CO
Built in 1889, 2nd oldest federal hatchery still in use. Nature trails, tours, panoramic views.
Mesa Verde National Park
Mancos, CO
World Heritage Site of Anasazi cliff dwellings dating to 1200 AD. Guided tours.
Monte Vista National Wildlife Refuge
6 m. S of Monte Vista, CO
Unique wetland habitat in a desert setting. Wildlife, migratory waterfowl, self-guided tours.
Pawnee National Grassland
Briggsdale, CO
Pawnee Buttes, eastern Colorado Plains: lots of Dust Bowl type rangeland
Rocky Mountain Arsenal
Denver, CO
Former munitions plant is now a wildlife sanctuary. Access only by scheduled guided tours.
Rocky Mountain National Park
Estes Park, CO
Small glaciers and volcanos, 91 peaks over 11,000 feet, Longs Peak (14,255 ft.) Trail Ridge Road, 355 miles of trails.
Sand Creek Massacre National Historic Site
Eads, Colorado
2,385 acres
Site of an 1864 massacre of mostly unarmed Arapaho and Cheyenne women, children and elderly men.
Sangre de Cristo National Heritage Area
Alamosa, Colorado

Historic area encompassing three National Wildife Refuges, Great Sand Dunes National Park, San Luis Lakes State Park, Zapata Falls National Recreation Area and more.
Ute Mountain Tribal Park
Towaoc, CO
Primitive area with Anasazi ruins in various stages of reconstruction.
Yucca House National Monument
Visitor Center at Mesa Verde National Park, Mancos, Colorado
9.5 acres
No public access.