The primary mode of public transportation for most areas of San Francisco - BART and the Muni Metro are faster and more frequent, but sparse in coverage.
Deriding Muni is a local past time - complete with a diary - but the system usually works if not quickly.
Most buses have bike racks, some not, or they're full (2 bikes max)... but hey - it's a bike - figure something out :)
Most bus shelters have a map of the whole Muni system. Next bus provides live updates, with varying correlation to reality.
Beyond individual cash-only fares, there are a variety of passes available, including the flexible Clipper card. CityPass also includes a 7-day pass, among other things.
Website: http://www.sfmta.com
Wikipedia: http://en.wikipedia.org/wiki/San_Francisco_Municipal_Railway