I'll second the reccomendation to do Pt. Reyes with the added note that it's further away from the city than you might think.

You should also try and get to Muir Woods to get a small feel of the redwood forests farther up the coast.

I'll agree with going to Oakland Harbor as well- I had a great hamburger there a few years ago.

If you want to travel a bit south of the city Montara is fairly close with Pigeon Pt just a bit further south and if you want to make a full day of it add Santa Cruz with it's two lighthouses.

Dennis