These are all great suggestions/places to go. I really have nothing 'great' to add, but I will try.
-take a ride on a cable car
-if going across to the bay (Berkeley, Oakland) check out the new bridge they are building...or take BART.
-rent a car and drive down Lombard Street
-walk across Golden Gate Bridge (or at least half way)
-check out the Exploritorium (might be fun for your three year old)
It is amazing that you guys know so much about SF and all of its attractions.
It is sad that I know so little...and I was born/grew up there.
PS: I have never been to Alcatraz