Online transit planners have come a long way (especially in the bay area) but they still aren't perfect.

511.org covers many agencies in the 9 counties with the exception of some spots in Marin. Click here for a complete list of coverage.

Google Transit includes 5 of the bay area agencies that are limited to the city of San Francisco (Bart, Muni), the East Bay (AC Transit) and a couple of others (VTA, Caltrains)

Using sites like Transit & Trails will help to encourage the improvement of these online tools.