National Scenic and Historic Trails
Near Brown's Pass in Glacier National Park, on the Pacific Northwest National Scenic Trail
California National Historic Trail
City of Rocks National Preserve, Idaho
So far, the list below is what I have found for designated National Trails: most multi-state, some historic, some scenic, some both. The Ice Age Trail and the North Country Trail are relatively new. Both are incomplete, so far. The Continental Divide Trail started out maybe 50 years ago, following that top line of the Continental Divide from Canada to Mexico, and is also still incomplete. The Lewis & Clark National Historic Trail is a new project from the National Park Service. While I was attending the National Scenic Byways Conference in Denver (August, 2009) I met a fellow who was involved with getting Lewis & Clark off the ground. He told me they were still mapping out the route and negotiating with private land owners along the way, so it might be some time before the entire corridor is laid out. There are similar things going on with the Old Spanish Trail and the Juan Bautista de Anza Trail.
The Santa Fe National Historic Trail has issues of its own. In the summer of 2009, a horse race was run from Santa Fe to Missouri, following the old route as much as possible. One of the stops on the original Trail was at Fort Union in Watrous, New Mexico. Fort Union National Monument doesn't allow horses on the property so they had to run the official race (even with all their official sanctions) around the Fort Union property. I would imagine there were other places along the old route with that kind of problem, too, like that area of Colorado where the Army's Piñon Canyon Manuever Site is located. And John Martin Reservoir (on the Arkansas River) has flooded most of the original trail in that area. A lot of the trail across Kansas is now private property and used for the growing of wheat and other grains.
The Nez Perce Trail and the Iditarod Trail have "wilderness" problems. The Nez Perce Trail found a solution when the Selway-Bitterroot Wilderness was designated as separate from the Frank Church-River of No Return Wilderness in Idaho. What separates the two is a 60-foot wide corridor along the Magruder Road, a doubletrack 4WD dirt route that faithfully follows the original route the Nez Perce followed across the Bitterroot Mountains during their famous run back in 1876.
The original route of the Iditarod runs across a large piece of the Innoko National Wildlife Refuge and Innoko Wilderness Area in Alaska. So when you are watching that race on your favorite dog sled sports station, realize that they are routing the race around the wilderness area on trail cut specifically for the race (one route for odd-numbered years, another route for even-numbered years). US Fish & Wildlife has a proposal on the table to tunnel a route across the wilderness area so that the true trail can be managed and maintained (and used for the race), but that brings up questions about preserving the old gold mine camps that also exist in the woods along that route through the wilderness: the rules regarding wilderness specifically forbid the use/presence of motorized or mechanized equipment (including chainsaws and snowmobiles) inside the boundaries of any designated wilderness (although there are certain exceptions for the use of motor boats and aircraft in certain areas of certain wildernesses).
Note: the list below does not include the vast majority of National Recreation Trails as that list is very long.
Along the Pony Express National Historic Trail in western Utah
Lower photo is courtesy of the Bureau of Land Management