Recently we went to San Francisco Golden Gate Park for my mother's birthday. Her primary focus was The Conservatory of Flowers, which is an interesting mix of exotic plants, and local fauna. The small admission fee was worth the 30 minute visit. The hardest part was finding parking. I suggest arriving fairly early (latest 10am) in the morning on weekends to avoid looking around. As of 2004-2005, the California Academy of Sciences and adjoining Steinhart Aquarium are temporarily moved to an off-site location (near Zeum). They are working to revamp the museum. I believe they should be back to Golden Gate by 2006.
On another trip to San Francisco, we spent a day at the Exploratorium. The Exploratorium is a hands-on science museum covering all facets of science. This was a lot of fun, and there are a large number of age-appropriate activities. My daughter loved the shadow wall. In a sheltered room, you could pose against a wall, a timer would go trigger a flash and your shadow would be frozen for 10 second to look at. Parking was easy in the adjoining parking lots. A close eye on those toddlers. Rainy days bring out lots of people and little-ones can easily get lured into a bright and shiny exhibit across the way. Make sure to walk around to the Palace of Fine Arts while there. Maybe you'll show up in someone's wedding pictures!
More? How about visiting the San Francisco Zoo? The San Francisco Zoo is a member of the AZA. This means if you have membership with one of these partner zoos (like Sacramento) you can get in for a discounted admission and wait in the much shorter "Members" line. The zoo has a nice collection of animals, but nothing like the San Diego Zoo. Bring some cash for parking (if you use the lot, limited street parking is available) and the carosel. The cafeteria takes plastic, but the food options are rather boring. There is a beach across from the zoo, which has many broken sand-dollars. Name?? Sorry.
After the zoo, we typically head down to Pier39 or Ghiradelli Square. Fun but a lot of walking. The Pier39 carousel would not let toddlers ride without a parent, and made the parent also pay. What? Go see the Sea Lions. I've heard the Aquarium is not worth the $$$.
@Ghiradelli Square expect a lot of stairs to climb for a few interesting stores. You'll be carrying that stroller more than pushing it. Lots of "You can look but don't touch" said. I'd suggest you head straight to the ice-cream parlor. Have an idea of what you want as you order right inside the door, then take a seat. People appeared to come in waves, and seating was available on intervals.
As with any trip to San Francisco, the weather can be completely random. We've left rain in Sacramento, and arrived in San Francisco with sunshine. We've also arrived in San Francisco with rain, fog and simply overcast.