[STeeLy]

I actually stayed near the airport in San Bruno, within walking distance of CalTrain (5 minutes) and the BART station (10 minutes).

I almost prefer CalTrain to the BART. While it doesn't get you directly into downtown, it is about a half hour walk away from the Ferry Building along the shore line. You can also catch the MUNI Streetcar from across the CalTrain SF terminal. CalTrain also gets you into San Jose right near the SAP Center if you want to go watch the Sharks.

If you plan on visiting the the Golden Gate Bridge, there is a free way to get there from Downtown SF. Look up PresidiGo shuttles/buses, it'll take you into the Presidio (Palace of Fine Arts area), then you can switch into another PresidiGo shuttle and it'll drop you off right at the parking lot to the Golden Gate Bridge Visitor's Center. The Presidio is a nice area to look around as well I think.

Fisherman's Wharf is touristy and the prices reflect it, for food if you want to stay in that area, I'd head over to Pier 39 (where all the seals are), prices are a bit better.

I've heard of people biking across the GGB to Sausalito and taking a ferry back. If you're like me and are a cheapskate, be careful which ferry you catch, Blue and Gold Line ferries are about double the price compared to Golden Gate ferry. Blue and gold drops you off at Fisherman's Wharf, while Golden Gate Ferry goes to the Ferry Building.

I didn't have time the last time I went, but I would have loved to go to the USS Hornet Museum in Alameda