In addition to the industrial narrow gauges already mentioned, there was also the salt pond railroads at Newark and Redwood City. The remains of the Redwood City operation were still very visible several years ago.

Years ago, someone told me about a narrow gauge brickworks railroad in East San Jose that suppossedly survived into the early 1970s.

Of course, in the early 20th century, we also had the South Pacific Coast, North Pacific Coast and the California and Nevada.

And there are always the SF cable cars and Roaring Camp, the last "full size" ng operations I can think of in the Bay Area.