My husband and I want to fly out for a few days at the end of September and see the Pacific ocean, and the redwood trees, but that’s all we’ve decided so far. We will probably only be there 4-5 days, or else I’d be tempted to try to get up to Seattle too.
We are interested in nature, history, and art. Should we see San Francisco? Are there any old west sites nearby that aren’t totally touristy? All suggestions welcome.
Will you be renting a car? It is not absolutely essential to have a car if all you’re visiting are things in San Francisco, but IMO, it is if you wish to visit anything outside of the City proper. You are at least, picking the, IMHO, absolute best time to visit Northern California. The omnipresent fog usually takes a break during September/October, and you can actually see postcard-like vistas.
For nature, I’ve liked visiting the Steinhart Aquarium in the past. If you can spare the time (about a 3 hour drive south from SF), the Monterey Bay Aquarium is one of the finest on the planet. For redwoods, Muir Woods is 11 miles north of the Golden Gate Bridge. (Which you should consider walking across; the views are incredible.) I have not seen the redwoods at Muir, and I don’t believe there are that many there, but then again, Avenue of the Giants is very far away.
Art: SF MoMA is fun, easy to get to, and worth your time. Here’s the SF CBS affiliate’s list of the best museums in SF.
‘Western’ history? I am drawing a blank. There’s always visiting Alcatraz and Angel Island, but I’m not sure that’s what you’re looking for. Sutter’s Mill is a bit of a drive from SF. Perhaps the Wells Fargo Museum in SF? I’m sure the San Francisco Museum and Historical Society can provide you with other recommendations. The GLBT museum in SF’s Castro district, according to its site, “is the first full-scale, stand-alone museum of its kind in the U.S.”
Oooh, I know! How about visiting one of the old California Missions? Mission Dolores is right in SF.
Beautiful city; I’m envious of your trip.
We just got back from a week in Napa. If you like food and wine, it’s the place to go…
There’s also a really interesting modern art collection (mostly from Bay Area artists) at the di Rosa - well worth visiting if you like this type of art.
Muir Woods is very nice, if a little touristy. It’s got maybe a mile of paved and boardwalk walks through the oldest and tallest trees, filled with camera-wielding tourists. But it is definitely the closest impressive stand of redwoods to San Francisco, so it should be on your list.
See the Cable Car Museum in San Francisco. It’s only a couple of blocks from Chinatown, and you can actually see the giant wheels turning the massive cables. It’s totally free, so be sure to stick a couple bucks in the donation boxes. Eat in Chinatown or in Little Italy; they’re right next to each other and very pretty.
Napa is wonderful if you like food and wine, and can afford to spend a the money. It’s out of my budget, personally.
I don’t know how far north of the city you’re intending to go, but I’d really recommend the Lava Beds National Monument if you’re going up near the Oregon border. They’ve got about one hundred miles of caves, if I recall correctly, and since they’re all very new, geologically, there’re no delicate formations to damage, and so there are no guided tours of any kind. The caves are totally undeveloped, with no paths, lights, or handrails, and so you just grab your flashlight, maybe a helmet, and go exploring!
If you are based in SF, Coloma is about 2.5 hours drive (in light traffic) to the foothills outside Sacramento. There is also a nice wine area in El Doradoand Amador counties that are not touristy (most do not have tasting fees, and there are few busses). Bundling together could make a nice day excursion.
Otherwise, **Gray Ghost **and the others provided a good list of to-dos.
A bit in the History department:
(1) Golden Gate Bridge / Fort Point. Bona fide Civil War era fort, built at the mouth of the San Francisco Bay, at a time when it was feared that there would be Civil War activity there. Park in the lot at the south end (San Francisco end) of the Bridge (good luck finding a parking place), and it’s right there.
(2) Next, drive across the bridge. Notice the mountain immediately at the north end of the bridge, on the right. Take the first off-ramp after the bridge (just after the touristy vista point), and drive up that mountain. (It’s called Fort Cronkhite.) FABULOUS views over the bay, the bridge, and S. F. – clear weather permitting – almost like a view from an airplane. Along this road are several ruins of WW II era fortifications, including an abandoned artillery emplacement at the top.
This puts you into Marin County, so you are already on your way towards Muir Woods. For a good scenic drive, find your way back to Highway 1 and drive up the coast for a while, say, to the mouth of the Russian River. Turn inland there, and drive on that road, through redwoods, all the way to Santa Rosa or any town in that area.
This takes you through redwood forest, including the town of Guerneville. There are some beaches there along the Russian River. There is also a side road there, leading to Armstrong Woods, a redwoods park where you can picnic or hike, with trails of varying difficulty.
From Santa Rosa, there is a somewhat back-country road leading through the hills to Calistoga. (I trust you will have maps or GPS or whatever to find all these roads.) Half-way along that, there is another nearby side-road that passes by a genuine petrified forest. There is a private piece of land there where you can pay a few bucks and go in and take a brief hike through the petrified logs laying all around.
In Calistoga (you’re at the northern end of Napa Valley now), you can poke around. It’s a kinda picturesque but touristy little town. Being at the foot of an old volcano with hot springs, it’s famous for spa resorts – they are in just about every block. Get yourself a good full-body massage. If you’re there as a couple, you could get the full treatment – couples massage, mud bath, facials, the works, if one is into that.
Ask for directions to the Golden Haven spa, which is a bit off the main drag. Ask if Betina is still there!
Then, take Highway 29 south, back toward San Francisco. This runs through the heart of Napa Valley, so you can stop in every little town and tour the wineries. (Although back in Sonoma County, where you were earlier in the day, there are plenty of excellent wineries too.)
That should keep you busy for a day. You’ll see PLENTY of Pacific Ocean, redwoods, and other goodies on this day trip.
Oh, and by the way . . .
If you take the advice of any responses in this thread, you are REQUIRED to come back and post one or more detailed reports of your vacations for the rest of us to vicariously enjoy! 
If you like beer, go to the website and arrange for a tour of the Anchor Steam brewery.
Here are links to two other recent threads full of suggestion for visiting San Francisco and surrounding areas:
Those OP’s didn’t specifically ask about nature, history, and art, so they got all kinds of suggestions, but there’s a lot of nature, history, and art among them.
ETA: SERIOUS DATA CORRECTION: Where I wrote above “Notice the mountain immediately at the north end of the bridge, on the right.”, I meant “Notice the mountain immediately at the north end of the bridge, on the LEFT.” When you get off the freeway just past the touristy vista point, you then have to drive under the freeway to the other side to get to it.
Outside of the city itself, the coast, anywhere between Big Sur and Point Arena can’t be beat. There are beautiful bluffs and beaches, deep forests, and funky little towns all along the way.
If you want to see more than just redwoods, Calaveras Big Trees is a great place to see our other giant trees. The Gold Country and western Sierra foothills is another great NorCal area to visit.
If you want pretty country, old west, and not a lot of tourists, head east over to Highway 49 and visit Columbia*. Restored Gold Rush mining town. Highway 49 runs along the west side of the Sierras through some of the prettiest country in California.
I can’t fault Napa, SF or the other suggestions in this thread, but for old west Columbia and 49 have them beat hands down.
*It will be a lot closer if you fly into San Jose, Modesto, Merced, or Fresno Air Terminal (Airport code FAT :))
Senegoid, I am going to have to validate each and every one of the points on your itinerary. When are we going? 
Thanks for all the great suggestions, guys! I will probably do some of these, and definitely report back with pictures.
One other thing I was seriously considering was a whale-watching expedition, but my research indicates that a lot of people get seriously seasick on these trips. I don’t think I would,but my hubby used to sleep clinging to the side of our water bed. Sigh. Maybe I’ll ditch him at a museum and go without him.
Absolutely perfect! Fort Point is a do not miss. Although I might take a jig left around Santa Rosa and go out toward the coast and see Fort Ross if you like western stuff. A choice between that and Calistoga would be tough, but they’re both so different that I’m sure one or the other will make you happy.