Here is a new Bay Area Rapid Transit Map which joins some other BART maps already listed here on Google Maps Mania (Search in-page for BART). This BART map has a great way to select stations and interact with them by zooming in and out easily, link directly to the official BART webpage for that station and also view the full schedule for that station. Map markers are multi-colored if several stations are served by that line. To use the mashup to plan a trip between stations, click on the 'Plan Trip' tab, select two stations and the calculator will tell you the departure and arrival times, along with the travel and time and fare. I wonder why is it taking municipal transit authorities so long to catch on to technology such as the Google Maps API?
More Google Maps Transit Maps Here (look right)