Operated by the Pacific Locomotive Association, the Niles Canyon Railway uses the ex-Southern Pacfic right-of-way which was the first transcontinental railroad into the Bay Area. They operate excursion trains on weekends (check the web site for schedules). Note the historic bridges on the route.
On the other side of the canyon is the UP (ex-WP) mainline which is fairly active. The Altamont Commuter Express (ACE) trains use this route.