Cenozoic geology seems easier to put into numerous boxes than older geology (although of course there's a lot of overlap, like glacial features being reworked by rising seas, or volcanic flows later being eroded into unusual topographic formations). The major advantage is that Cenozoic deposition and erosion have overprinted, destroyed, or buried the pre-Cenozoic examples of most of the categories listed below. Jurassic caves have collapsed or been buried. Cretaceous canyons have been filled in. We can point out rocks left from Paleozoic barrier island complexes, but we can't watch the Paleozoic ocean roll in. Some of the Cenozoic processes and features we can observe in National Park Service units include the following:
CavesCenozoic cave-forming processes have produced the subterranean features of some of the most famous parks, including Carlsbad Caverns National Park, Mammoth Cave National Park, and Wind Cave National Park. Caves don't last forever, of course, being vulnerable to collapses and filling in. Two notable examples of filled Pleistocene caves were found in locations now in parks: Cumberland Cave (Early Pleistocene, Potomac National Heritage Trail) and Port Kennedy Cave (Middle Pleistocene, Valley Forge National Historical Park).
Late Cenozoic coastal processesThe barrier islands flanking the East Coast and Gulf Coast owe their existence to postglacial sea-level rise. Among them are Assateague Island National Seashore, Cape Hatteras National Seashore, Cape Lookout National Seashore, Fire Island National Seashore, Gulf Islands National Seashore, and Padre Island National Seashore.
Glacial processesThe obvious parks associated with glaciers are, of course, Glacier National Park and Glacier Bay National Park; if you go beyond those with "Glacier" in their name, you might also add the other parks of Alaska, North Cascades National Park, Olympic National Park, Rocky Mountain National Park, and Yosemite National Park. Several other NPS units show the aftereffects of glaciation. We've already seen a few of the effects in Mississippi National River and Recreation Area, including waterfalls and the crushing of unfortunate rodents. The various parks ringing the Great Lakes owe their existence to glaciation, including Apostle Islands National Lakeshore, Indiana Dunes National Lakeshore, Isle Royale National Park, Pictured Rocks National Lakeshore, and Sleeping Bear Dunes National Lakeshore. There is also a trail dedicated to Ice Age features, Ice Age National Scenic Trail. On the East Coast, we see locations where glacial products are being reworked by the ocean, in places like Boston Harbor Islands National Recreation Area and, most outstandingly, Cape Cod National Seashore, which is essentially piles of glacial debris that have been artfully sculpted by the rising Atlantic.
Marine rocks and sedimentsAlthough the great interior seaways drained away from North America following the uplift of the Rockies, some of the coastal areas of the U.S. have been periodically inundated. In the East, several parks declared for historical resources are also situated on Cenozoic marine deposits, and include some of the first sites studied for fossils in North America. Among them are: Colonial National Historical Park, where the Pliocene-age Yorktown Formation was first described; several units in the Washington area, such as Fort Washington Park, Piscataway Park, and Suitland Parkway, featuring the Late Paleocene-age Aquia Formation, the Early Eocene-age Nanjemoy Formation, and the Early–Middle Miocene-age Calvert Formation; George Washington Birthplace National Monument, situated in an area of older Early–Middle Miocene-age Calvert Formation sediments; and Petersburg National Historical Park, featuring another historic area of Yorktown Formation exploration. To the southeast, Vicksburg National Military Park coincides with historically notable outcrops of Gulf Coast marine rocks in the Early Oligocene Vicksburg Group.
On the west coast, four parks provide outstanding records of the Cenozoic in convenient reach of Los Angeles or San Francisco. They are Channel Islands National Park, Golden Gate National Recreation Area, Point Reyes National Seashore, and Santa Monica Mountains National Recreation Area. You've probably never heard of these parks in terms of their geology, but they are some of the best-kept geologic secrets in the National Park System, featuring unusual tectonics (ever wondered why the Transverse Ranges of southern California go east-west instead of north-south? They got pulled out of place in the mother of all LA traffic jams, between the North American and Pacific plates), volcanism, metamorphism, terrestrial and marine deposition, and a variety of fossils, including the pygmy mammoths of many posts ago.
[Added 2015-01-18] Glacier Bay National Park, mentioned above as a glacial park, also has several marine formations deposited from the Middle Oligocene to the Early Pliocene.