In the city:  

• Go to the San Francisco Bay Ferry - San Francisco Ferry Building Terminal on Saturday for the Farmer's Market, lots of great food stands and people watching
• Walk down Crissy Field to Fort Point Lighthouse, get a coffee at the Warming Hut, walk by the Palace of Fine Arts before/after (close by)
• Go to a Giant's game at AT&T Park
  
• If they're into art, visit the Legion of Honor and walk around Lands End afterward
  
• Check out Golden Gate Park San Francisco for lots of fun/random stuff like the Bison Paddock, Stow Lake, DeYoung Museum Sculpture Garden, Japanese Tea Garden, and Conservatory of Flowers.
• If they're picking up the tab, eat at good restaurants like Frascati, Kokkari Estiatorio, Frances, Locanda.

Out of the city (north):

• Go to Marin for a hike. Muir Woods is great but crowded.  Try something like Matt Davis Trail or something closer to Stinson Beach for beautiful coastal hike.
• Go to wine country.  I love the Napa Valley wines but its a bit of a circus.  Sonoma County is a bit more low key.
• Take a ferry to Angel Island State Park, bring a picnic and walk around a bit, amazing views
• Go shuck oysters in Tomales Bay
• A little far for a weekend but Lake Tahoe in the Summer is amazing.

Have fun.

Cross the Golden Gate Bridge once day (by car, bike, or walk), then drive over to Muir Woods which is a beautiful old redwood forest. You can spend an hour or several walking/hiking easy paths. If you love great views, drive up to Mt. Tamalpais which is close, then have a leisurely lunch in Sausalito CA. Stop at the Marin Headlands on the way back for amazing views of San Fran and the Golden Gate.

I also love driving through the Presidio and stopping for a walk on Baker Beach. It's a beatiful area and drive. From here, it's easy to do to the old Sutro Baths. My dad actually swam here as a kid (a long time ago). Now, it's just ruins, but it's beautiful, interesting, has a nice beach area, and great walking trails (though a lot of stairs).

You could also spend a day playing at Golden Gate Park. Check out their website. It's HUGE. They have gardens and museums, an aquarium and paddle boats. It's a beautiful place to take a picnic and just enjoy it. http://sfrecpark.org/parks-open-spaces/golden-gate-park-guide/

Go to Chinatown, San Francisco or just have really amazing Chinese food. There are a ton of really great places. And if you love pizza, check out our family favorite, Gaspare's Pizza which is another old SF icon.

There's the Coit Tower which is seen and easy to combine with Lombard Street if you want to do the touristy things too. I also love the 16th Avenue Tiled Steps Project which is off the beaten path, but a nice walk and a beautiful little gem in the city. For more views, also go to Twin Peaks though it's nearly always foggy. You can also easily fit in the Painted Ladies, beautiful victorian era homes painted in bright colors, and another SF icon.

I love nature, so my favorite thing is to just start at the Golden Gate of the Presidio and hug the coast as much as I can all the way down. Do enjoy hwy 1. There are some beautiful places to stop along the way south there as well.

During my trips to San Francisco I always enjoyed a walk or run in Crissy Field I also saw a lot of people who rented bikes as well. It has a beautiful view of the Golden Gate bridge and a cafe as well. 

My mom & dad aren't super active so when they first started coming to visit I was often looking for stuff that would be fun but not too taxing.

A couple of things that were huge hits with my folks:

1. People watching in North Beach. Meandering around the few blocks around Washington Square Park was great. It's relatively flat and is very SF feeling. Cafes and coffee shops line the area and it's a great place to sit outside with a glass of wine or cup of espresso and soak up the atmosphere.
   
   If you like, you can take the MUNI 39 bus from Washington Square up to Coit Tower. It just reopened with all the murals restored. Wonderful.
   
   
2. And I second the idea of wine tasting in one of the regions that isn't Napa. Sonoma / Russian River wine tasting is great. It's much more low-key and with you'll find many fewer jackasses than at the Napa wineries. Also it's gorgeous and the wines are excellent.
   
   

If your parents are active I'm sure you'll be able to make use of the great ideas for hikes and outdoor destinations suggested by folks above. If not, or if you need a slow day, perhaps one of these options will suit.

Have a great time with your parents!

So fun! Definitely rent bikes on The Embarcadero and ride out along the wharf / Presidio and across the Golden Gate Bridge! You can even go across to Sausalito and ferry back. Go to the ferry building farmers market and try every sample, and eat at Cheesecake in Union Square on top of Macy's. Get a cone at Twirl & Dip in Golden Gate Park! See some of the fun I had with my parents here! 

http://www.welltraveledwife.com/2014/03/my-moms-favorite-thing-to-do-on-trip.html

Just these notes.  If the weather is good a drive over the Golden Gate Bridge is fantastic!  I have also boarded the ferry from San Francisco to Sausalito, spent some time checking out the shops and eating spots and then tanking a ferry back to SF.  You go right by Alcatraz on the ferry!  Walk SF and ride the Cable Cars!  

I highly recommend Carmel. Very beautiful beaches and a cute downtown to shop in. There is a neat 17-Mile Drive that takes you along the coast with lots of nice views of the water. Towards the end you arrive at Pebble Beach Golf Course. I recommend having a bite to eat at their outdoor patio if you can fit that in.

Capitola is another great idea.

Down Highway 1 far enough are great spots for berry picking.

I love tidepooling near Half Moon Bay