San Francisco is one of the largest cities in the USA. Its trademark image is that of the Golden Gate Bridge, which is often featured in comics to show the city in a simple and effective way.
In the DC Comics universe the post-Crisis reintroduction of Captain Marvel occurred in the mini-series Shazam! The New Beginning. The Teen Titans have their Titans Tower in San Francisco Bay. It is also home to one of Zatanna Zatara's mansions, the other being Shadowcrest.
"The San Francisco Waterfront, where the commercial concerns of nations and corporations meet and cross... and thus is a no man's land belonging to many interests, many ambitions, but hospitable to none" -- said in The New Defenders Vol.1 #133 (Jul1984).
Recently, the X-Men and a majority of the mutant community has moved to San Francisco. The X-Men saved the city during the Skrull Invasion. The Mayor is in complete support of their residency. After the destruction of their San Fransisco base, the mutant community moved to Magneto's abandoned Asteroid, now coined the Island of Utopia, which floats just off the Coast. A lot of damage happened to the city during Second coming, but the X-Men have been repairing the damage done by Bastion.
Star Trek Universe
Star Trek has been produced by many comic companies so it has its own entry. San Fransisco is an important part of the Star Trek Universe as it is the location of Starfleet Academy. Every Federation officer goes to Starfleet Academy.
With the recent release of Charmed Comics, it is shown that the Charmed Ones reside in San Francisco living in the Halliwell Manor, 1329 Prescott Street.