maps.google.com/bayarea

I saw this Google ad on the MUNI bus I take for commuting (yes. I take a MUNI and company shuttle to commute to Sunnyvale from SF!) and tried it and like it a lot.

This is a nice additional feature on Google Maps that gives you step-by-step transit directions including estimate travel time. It covers MUNI, BART, CalTrain, etc. also walking route. (but it looks like ferry is not covered).

Google Maps Bay Area Transit