Here's what I would recommend for a family trip to the city.
Note: You can skip this narrative and jump down to my photo journal below.
Where to stay
This was our second stay at Cavallo Point -- a resort housed on the former Fort Baker army base just across the Golden Gate Bridge. Why did we go back? I'm not sure where to begin. Let's start with family friendliness. The hotel welcomes families (as well as dogs of all sizes) with open arms. It is very well appointed, but not super fancy or stodgy. You can get dressed up to dine or just show up in your sightseeing clothes or active wear. No one seems to notice or care. The lodging houses are surrounded by Golden Gate National Recreation land with stunning views of the city, bay and the bridge. After a busy day touring the city, you can return to the hotel and have a complimentary glass of wine or two or grab a hand-crafted cocktail from the Farley Bar. Sit on the rocking chair front porch while your kids run freely on the front lawn. As much as we love the energy of being in the city, there is much to be said for being on the water where your kids can play outside. The concierge has a collection of balls and Frisbees available to use. Kids can choose to eat from a kid's menu for $10 a meal. The food is delicious. Younger children can visit the Bay Area Discovery Museum located at the foot of the property (admission fee not included). Other amenities: complimentary coffee and pastry station every morning, free yoga class most mornings, free parking, a shuttle to and from the ferry station in Sausalito on a regular schedule throughout the day. You can also get a ride into the city at 9:00 and get picked up at 4:00. If you need a break from your family, you can indulge in some spa treatments or relax at the Tea Bar in the Healing Arts Center & Spa or take a cooking class at the Cooking School. One of my favorite things about the place is the fresh scent of lavender and eucalyptus wafting through the air everywhere you go. Bliss. I can't say enough good things about Cavallo Point. We would definitely go back.
What to do
So much to do, not enough time. We had a car, which made some activities easier than if you were without one. Tip: Do not drive your car into the city. Traffic and parking are a nightmare. Walk, bike, cab, Uber or take public transit.
To make this as brief as possible, here are my top ten things to do (in no particular order) if your time is limited:
1) Visit the Exploratorium. It is a must. Plan to spend an entire day there. Your ticket allows you to enter and reenter as much as you want on the purchase day.
2) Walk or bike ride across the Golden Gate Bridge. Note: It is really loud on the bridge, which might scare some kids. Have a back up plan if you think this might be an issue for your family.
3) Take a break from the city and enjoy it from the other side of the bay. Take a ferry ride to Sausalito and explore on foot or bike.
4) Visit the Ferry Building. Learn about its history. Eat and shop there. Tip: Do your shopping at the end of the day and bring some large reusable shopping bags with you. Bags are hard to come by and you are charged extra at most places for a paper bag. Most are small and unwieldy. You'll see the local ladies shopping there with chic market baskets filled to the brim with fresh produce. Although tempting, buying one of those expensive satchels would only be a pain to travel with later.
5) Climb the stairs to Coit Tower and take in the best panoramic view of the city, bay and bridges. While you're there, check out the murals painted on the walls. Take time to stop and smell the roses and other flora in the secret gardens as you climb up and down the 400 stairs on Telegraph Hill that lead to the Tower. I don't recommend taking the stairs with small children.
6) Ride the cable cars! A visit to the Cable Car Museum is worthwhile for younger kids.
7) Visit China Town. Eat there!
8) Go see Lombard Street -- the crookedest street in the world.
9) Go to a baseball game at AT&T park and check out McCovey Cove.
10) Visit the sea lions on Pier 39.
A few things to note. If you plan to visit, Alcatraz, which I highly recommend for older children, tickets are hard to come by. To be on the safe side, buy them well advance. The new Walt Disney Museum -- that we didn't have time to visit -- is more geared toward older kids and adults. We visited Golden Gate Park during our last visit, including the California Academy of Sciences. If your time is limited, research the various museums before you go, and choose wisely. The Exploratorium surpasses any other kids museum we've visited. Put it on the top of your list. You won't be sorry.
Excursions
If you have more than a few days and a car, I recommend these excursions:
1) Take a walk in the redwood forest in Muir Woods. There are trails for every age and energy level.
2) Visit The Marine Mammal Center in Sausalito.
3) If you have kids with "The Farm," aka Stanford, on their college wish list, go while you're in the area. In our case, we have two boys nowhere near college age who are college sports fanatics. So, we drove out to Palo Alto to tour it. Not knowing much about the University, I thought the tour was interesting. The campus is gorgeous, as are the zillion dollar homes and cottages in Old Palo Alto.
Where to eat
We compiled a long list of places to eat before our trip mostly based on recommendations from friends who have visited or lived in the Bay Area. That plan went by the wayside when we got there. We ended up eating close to where we were each day or close to the hotel with the goal of hitting at least one dining spot that served seafood, Asian, Mexican or Italian cuisine.
A few things to note before I offer my restaurant picks. I was really surprised that the seafood we sampled at most restaurants was meh at best. I can get much better quality and variety here in land-locked Atlanta. Also of note, we ate lunch at the highly acclaimed Vietnamese restaurant The Slanted Door at the Ferry Building. Having eaten at the restaurant's old location on previous trips, we were excited to visit its new digs. Unfortunately, the restaurant has lost its luster for us. In my opinion, it's living off its reputation.
Here are some restaurants I would highly recommend. All have kids menus. If you have picky eaters, these are good options for you.
Ferry Building Marketplace
The marketplace houses some of the best food in the city. I recommend a movable feast of samplings from the food stalls. My favorites are: coffee at Blue Bottle Coffee, the sour dough baguette at Acme Bread, cheese and sandwiches at Cow Girl Creamery, cupcakes at Miette and ice cream at Humphry Slocombe. Be on the lookout for TCHO chocolate bars in some of the specialty shops. The company used to give tours of its factory in the city, but they have moved to Berkeley. Try the Mokaccino -- milk chocolate mixed with Blue Bottle coffee. Tip: Seating inside the marketplace is scarce. What little there is, is hard to find. Some large communal tables, as well as counter seating, are located in the area just outside Peet's Coffee. Or, you can eat outside on benches if it's a nice day and you don't mind being surrounded by pigeons. Not an option for me.
Sausalito/Milly Valley...
Fish
Located literally on the dock of the bay in Sausilito, Fish serves only sustainable seafood plus fresh salads and more. Stand in line to place your counter order. Enjoy a glass of wine or a beer from an extensive list, or fresh squeezed lemonade served in mason jars. Be ready to pounce on a picnic table outside as soon as one opens. The servers will deliver your food there. The fish tacos were notable, but the chowder and fish & chips were our faves. Skip the BBQ oysters. Come prepared to stand in line, and have cash or check in hand. No reservations. No credit cards accepted.
Copita
When we asked the hotel concierge for Mexican restaurants recommendations, she sent us to Copita Taqueira conveniently located on the main drag in Sausilto. The atmosphere is warm and lively with outside sidewalk seating. Copita prides itself for serving traditional Mexican dishes using fresh seasonal ingredients. Lunch and dinner menus are 100% gluten free. Your meal begins with a complimentary jar of jicama & cucumber spears dusted with chile powder, lime juice and flake salt -- a refreshing combination of tastes and textures. The bar features an extensive selection of tequila, so be sure to order a margarita. The $10 house margarita was shaken and served at our table then poured over a single square ice cube (my fave). It was excellent. Tacos are available in orders of two or four, which makes it fun if you want to try several. The mahi-mahi fish and special pork tacos were outstanding. The braised short rib was very good, but I would stick with tacos next time. The very generous bowl of tortilla soup was delish. Keep that in mind if you plan to order tacos. My eyes were definitely bigger than my stomach. Reservations recommended on busy nights.
Poggio
Poggio Trattoria serves classic Northern Italian cuisine using seasonal locally sourced ingredients, including some grown in the garden on site. I met some people at our hotel who had eaten there the night before. One was a chef. If he was raving about it then I knew it was good enough for us. The restaurant was warm and inviting with outside sidewalk seating. You can order half or full size pasta portions. I ordered the pasta of the day, which was excellent. As were the kids pizzas straight out of the wood fire oven. My husband ordered the yellow fin tuna. It was very good, not outstanding. If we were to go back we'd skip the surf -- except for the divine poached rock shrimp butter leaf lettuce salad -- and go with some turf. The $69 grilled porterhouse steak (enough for 2-3 people) was tempting, but we couldn't talk the kids out of their pizzas. If you are child free and feeling casual, I would recommend sitting at the lively bar and ordering several pizzas and salads to share along with a few (or more) glasses of sangria from the vat sitting on the bar. Reservations recommended.
Buckeye Roadhouse
A local favorite since 1937, the restaurant cuisine is described as quintessential American with a California twist. It is named for the buckeye tree outside its back doors. The two-floor open concept space is warm and cozy with dark lacquered panelling throughout. It is a definitely a special occasion place, judging from the number of birthdays being celebrated around us. Nevertheless, they welcomed us in our very casual attire. There's something for everyone on the regular menu with a kids menu to boot. We rarely order chicken out, but our sever recommended the signature chile-lime "brick" chicken. It did not disappoint. The fish of the day was excellent as was the organic butter lettuce salad I ordered to accompany it. Topped it off with a classic gimlet. There's a smoker out back, so consider ordering something from that section of the menu, especially if you're from the south and have a hankering for BBQ. My son devoured the smoked wings. Reservations recommended.
Palo Alto…
If you're in the Palo Alto area, don't miss the Palo Alto Creamery Fountain & Grill. It's a retro diner that serves breakfast all day, as well as typical diner food. Go for the beef. The burgers and fries are excellent. I highly recommend the Reuben too. Time your visit right or plan to wait for a table.
Where to shop
If you live in a major metropolitan city, skip shopping on Market Street. There you will find the same department and apparel stores you have at home. The one and only shop I wanted to visit was Serena & Lily located in the chic Pacific Heights neighborhood. I was expecting a retail store, but it's a design center. Some bath and dining linens are for sale, but not much. The store is still worth a visit if you want to see firsthand color ways, fabric designs and rug samples, as well as inspect the quality and construction of the furniture pieces on display. You also get free fabric swatches that you would otherwise pay $2 each when ordering from the catalog.
My photo journal:
{Former Officers' residences now impeccably restored suites. Book all the rooms for large families & bring your dog too! Relax on your own rocking chair front porch.}
{Lots of places to relax and take in the sea and floral air at Cavallo Point.}
A visit to the Ferry Building is a must! 
{A steal $15 a bunch!}
{Pretty in pink.}
Beautiful fresh produce...
Confections at Miette. I love this shop! Get yourself a treat. Buy gifts for friends and family.
{Ginger snaps are winners.}
{So is the toffee.}
{Ginger bread cupcake with cream cheese frosting. So pretty and tasty. Get one!}
Wash it down with some Blue Bottle Coffee.
Time to walk it off. Head over to Telegraph Hill on foot. Enjoy the scenery as you walk up the 400 stairs to Coit Tower.
{Secret gardens abound.}
{Level upon level.}
{Stop and smell the amazing roses…}
{Peaking out everywhere.}
{Panoramic view of the city from Coit Tower.}
{Red lanterns.}
{Grab a cup of chowder and a shandy at Fish.}
{Dine al fresco.}
{Margaritas are a must. Shaken and served at your table.}
{Pork tacos are the bomb.}
It you're in the mood for Italian, head over to Poggio. Share some pizzas and salad.
{Poached rock shrimp salad my fave.}
Confucius says: "Wherever you go, go with all of your heart." Great advice for a visit to San Francisco.
The End.
What are your favorite hotels, things to do and restaurants in San Francisco?
Take the cable cars to China Town. Eat there!
Take the ferry to Sausalito. Check out the docks and get some sea food.
Walk or bike around. Eat at local restaurants. Copita Taqueria is an excellent choice for traditional Mexican.
{Cleanse your palette with cucumber and jicama spears.}
It you're in the mood for Italian, head over to Poggio. Share some pizzas and salad.
The Buckeye Diner in Mill Valley has a warm atmosphere and great food. Order a gimlet to go with your meal. You can't go wrong with anything on this menu.
{The Buckeye Roadhouse serving good food since 1937.}
{Gimme a gimlet please.}
Don't expect to score any sales at the Serena & Lily design shop. It is very well appointed and worth the visit for viewing and free fabric swatches.
{Lovely Serena & Lily design shop. Table and bath linens for sale. Don't expect to buy anything else.}
If you make it out to "The Farm," stop by the Palo Alto Creamery Fountain & Grill for some diner grub.
{Reuben!}
{Stop by and say hi to Confucious in China Town.}
What are your favorite hotels, things to do and restaurants in San Francisco?
