Outside the Golden Gate, you often can see the pilot boat (purple) waiting for ships coming in and briefly converging with each ship to transfer the pilot. You can also see pilot boats taking pilots off of ships that are heading to sea.
South of the Bay Bridge, the San Francisco General Anchorage is usually full of tankers (red) and cargo ships (orange). You'll see more cargo ships at the Port of Oakland and in Richmond, and tankers at the oil company pier north-west of Richmond's harbor.
In the central bay, ferries and tour boats (yellow) dominate. You can see the ships poking just out the Golden Gate and then heading back in, turning tightly around Alcatraz on their way back to San Francisco. The ferries to Larkspur and Vallejo are the fastest commercial ships on the bay.
There's tugs (blue) all over the Bay, escorting ships through the central bay, guiding them into docks in Oakland and Richmond, working on the bridges, and hauling barges.
For a complete list of all the ships our AIS receiver has logged (since April 2006), sliced and sequenced on request, visit the San Francisco Bay Ships page.