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This diner is close to the beach and zoo and offers an extensive menu of american diner faves with some asian dishes mixed in. Breakfast is served all day and portions are very generous. Great for fusy toddlers who only like pancakes or grill cheese all day long. Prices are affordable by SF standards. Also, this place is very family friendly and the servers are great.
The San Francisco Zoo is a great place to bring kids and enjoy a walk in their nicely landscaped grounds. Ticket prices are under $15/person and locals can really get a lot of use out of a year long family membership (around $80). We go at least once a month. Toddlers love the meerkat tunnels made for them, the little puffer train and petting zoo. The petting zoo is one of the nicest that I have ever been to. Bring your own lunch though, food is pricey and tasteless. Also, watch out for the squirrels- I watched one carry a sandwich in a plastic container off a stroller into the woods effortlessly.
The Randall Museum is a great place to bring toddlers. Aside from numerous low cost classes and activities for all ages, it houses interactive educational displays of interest to children and adults. Highlights include the fully furnished 1906 earthquake shack, a working model train exhibit run by serious train enthusiasts and petting area. Best of all it is totally free.