OMG I can't believe your staying in Alameda LOL.. that is where I grew up for 20 years
Such a cute little town..
Lombard St.
Cliff House Restraunt in SF has a great view of the water, and there is old bathhouse ruins right there, along with a cave type dealio through the rocks with a great look out there.
John Muir Woods is always good but it's kind of a drive but it's close to the CliffHouse.
Everything else mentioned here is a must see too, there is so much to do there! I tried to mention different stuff then what was already said
SFMOMA is great!
I love the Bay Area...