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). According to a local article about a recent lawsuit by the town about the ownership of this line dating back to 1925, the lines were "operational" until 1998, although there have been no reports of trains on the line since 1996.
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.