We love Jackson Square, which is close to the SF waterfront, notably the original location of Ghirardelli Chocolates (founded in 1853, where Ghirardelli lived upstairs with his family!) 
Things have changed over time, of course, and now Jackson Square is a trendy area featuring many boutiques, shops, and galleries, such as Isabel Marant SF.
Docs Lab SF is a great music spot in Jackson Square.
