(covers information from several alternate timelines)
San Francisco Bay was an estuary on the west coast of North America on Earth. Together with the Pacific Ocean, the Bay formed the San Francisco peninsula. It was bordered on the west by the Golden Gate strait, the location of the Golden Gate Bridge. It contained a number of small islands, including Angel Island and Alcatraz. It also contained the San Francisco Bay Stadium.
In 2258 in the alternate reality, the Narada deployed its drilling platform over the inlet of San Francisco Bay, right next to the Golden Gate Bridge, and began drilling a hole toward Earth's core. The drilling platform was destroyed by Spock in the Jellyfish, its debris falling into the bay. (Star Trek)
In 2286, the captured Klingon Bird-of-Prey HMS Bounty crash landed in the bay due to the effects of the Whale Probe, but stayed afloat long enough to release the humpback whales George and Gracie. (Star Trek IV: The Voyage Home)