The Silicon Valley Public Transportation Wizard
Navigating the acronym soup of only Silicon Valley public transportation systems is much easier because of the 511.org TakeTransit Trip Planner. Just enter your starting point and destination, and it'll tell you not only what to take, but provide you schedule info and how much it will cost.
The system comes with a handy map of all the areas it covers. You'll not only find the basics like the VTA, SamTrans, BART, MUNI, and ACE, but also connections with the Stanford Marguerite Shuttle and the Golden Gate, Harbor Bay, and Vallejo ferries