Alameda, CA was a true railroad town -- it served as the western terminus for the original transcontinental railroad. It also served as a port for Southern Pacific railroad ferries. This port, or "Mole", was served by local trolley cars, railroad ferries to San Francisco, and local steam commuter lines of both Central Pacific and Southern Pacific. Upon completion of the Bay Bridge, the Alameda Mole was no longer necessary. Soon after, the Mole area formed the basis of the Alameda Naval Air Station, which closed in 1997.
Today, remnants of the original tracks and structures are easily found throughout Alameda.
Clement Avenue Branch: The Clement Avenue Branch was a short line that ran in the pavement of Clement Avenue, in order to serve local industries (see pictures below). A majority of tracks in this area of Alameda were constructed in 1918 by the city itself in order to grant rail access to a number of customers along its shoreline. Access was first given to the Southern Pacific Railroad via trackage rights. In 1925, the city handed control of the plant over to the newly-formed Alameda Belt Line Railroad, owned jointly by both the Athcison, Topeka and Santa Fe Railway and the Western Pacific Railroad, who continued to operate/maintain the tracks.
By the time the last shipper on the line closed down in 1998, the ABL was still operating under both BNSF Railway (successor of the AT&SF) and the Union Pacific Railroad (successor of the WP). The ABL then ceased operations over the line, and the city purchased the plant back from ABL in hopes of possibly continuing rail operations. However, at this point the tracks were in bad shape, and due to no prospective customers along the line, the City of Alameda and the Alameda Belt Line Railroad filed for abandonment of the entire route in 2012.
105th Avenue Branch: The south part of Oakland was a heavy industrial area, once served by the 105th Avenue Branch off of the SP/UP main line. Though abandoned, the tracks still remain in the area.
Thanks to Andrew Laverdiere for contributing information about this route.