Awesomely, the ferry services in Bay Area are quite a convenient and picturesque trip. From San Francisco, the Blue and Gold Fleet operates boats to wonderful places all over the Bay. The most popular ferry rides for visitors and locals alike are those to Angel Island and Sausalito.
Angel Island is beautiful and well worth a visit. Most of those traveling there for a day of hiking, biking, and picnicking are from the Bay Area, but everyone's invited. It's a remote little island void of traffic. You can hike around or hire bikes, but bring plenty of food, liquor, and some water, and don't forget to catch the last ferry back.
A century ago, tens of thousands of East Asian immigrants endured an ordeal at the immigration station at Angel Island (the "Ellis Island of the west") before continuing to the mainland. Most of the detention camps are still intact and guided tours are available.
If you've got nothing else to do, I suppose you might as well go to Sausalito. You're almost guaranteed a superb view of the San Francisco skyline, at the small cost of yuppies, high-end shops, and elite tourists. Many visitors choose to ride a bike from San Francisco over the Golden Gate Bridge to Sausalito, and then catch a ferry back. 
Additionally, the Blue and Gold Fleet runs trip to Oakland, Tiburon, and Vallejo, where a shuttle runs to Six Flags amusement park. 
You can find the Blue and Gold Fleet ferry scheudle here: http://www.blueandgoldfleet.com/Ferry/
