Sutro Project / Muni
Combining with BART for a poor man's subway system, the Muni (officially "Muni Metro") light rail works well for some routes. The vehicles run below ground along the Market St corridor and otherwise operate on the roads.
Most bus shelters have a map of the whole Muni system, along with somewhat reliable real-time info - also available here.
Wikipedia: http://en.wikipedia.org/wiki/Muni_Metro
