You might think of using BART. It runs from Fremont throughout the Bay Area.

For San Francisco, parking is pretty expensive. Public transportation in SF is fairly cheap and very plentiful.
Just look up SF Muni.

If you google to Oakland zoo, you can see easy public transportation.

That sounds great, it's going to be an awesome trip!

Here are are few things I can think of, that you could choose from:

1. South of Fremont, CA:

-Monterey, which is about a 1.5 hour drive, (southbound). There is a 17 mile scenic drive and a famous aquarium.

-Big Sur, a 45 min drive from Monterey (southbound)

-Hearst Castle, a 1.5hour drive from from Big Sur (southbound)

2. If you're going to SF, don't miss Fisherman's Wharf

3. Kind of off-topic, but may want to check out the Stanford campus, it's awesome

4. North of Fremont - I was going to recommend Redwood National Park, but that's too far I guess. It is an amazing place though, you just have to keep that on your "to do" list for some other time.

You'll will have a lot of fun!

If you go to the Golden Gate Bridge, you can also go to the Marin Headlands. Absolutely beautiful views. There's also a wildlife rehabilitation center there. The three year old might enjoy seeing some sea lions there.

If you come back to visit again and have time for a longer trip, go to Yosemite. But it's four hours each way so much longer than what you want to do this time. But it's a fabulous place to visit when you have more time.

On a clear day drive up to the top of Mt. Diablo. If lucky you'll have a view that goes from the Pacific to the Sierra.

Muir Woods and Mt. Tam makes a good combination for a day's outing.

Will you rent a car? Or do you want to do this trip only with public transportation?

What great ideas - thank you!
I had also thought about checking out Stanford & Berkley campuses. My husband is a tech-geek type so I found some cool computer museums south of Fremont with reasonable entry prices (in some cases, free) and a few science centres, but I think they may be too advanced for our child to get much from (then again, you never know what they're picking up on!)

I like the idea of a scenic drive, especially if it hugs the coastline! We're land-locked here, so if we want to see water we need to find a lake or river.

We will be renting a car - easier to get around with a small child (still in a car seat), especially if you'd like to go a little further away from 'home base'

You may want to check into the Exploratorium in SF. I think they have thing geared for all age groups.

Renting a car's a great idea, gives you much more convenience and freedom (i wasn't sure since you mentioned being on a budget).

Definitely do a day trip into San Francisco proper. The cable cars, Chinatown, Embarcadero, Fisherman's Wharf are definitely worth experiencing.

If scenery's your thing don't miss Muir Beach and Muir Overlook--5 minutes from Muir Woods, and about 30 minutes from SF.

Just got back and loved SF and the surrounding areas. We found very inexpensive motels w/free parking on Hotwire and Priceline.

If you're on a budget, make sure that your hotel includes parking. Some hotels charge as much as $60 just to park overnight.

Lawrence Hall of Science above the UC Berkeley campus is a great place to hang out with kids.

If you enjoy visiting college campuses, as my DH does, Berkeley and Stanford are outstanding.

A three year old is really too young for the Exploratorium, but the perfect age for the Bay Area Discovery Museum that's tucked under the Marin side of the GG bridge. Great views for the parents too. http://www.baykidsmuseum.org/

Fooey - lost another post getting this webpage. Anyhow - in addtion to driving on part of the 49? mile scenic drive around SF - you might also take a Ferry over to Sausalito - for a great view of the Bay, Golden Gate Bridge and SF Skyline.

And perhaps the biggest attraction of all is Golden Gate Park - and the young one might enjoy seeing the Bison/Buffalo (if they are still there) down by the beach - and in the middle of the park are Museums, Zoo, the Japanese Tea Garden, whatnot. http://www.golden-gate-park.com/

My Bad: Guess the Zoo moved years ago? see: http://www.sfzoo.org/plan-directions

And here is another page on Golden Gate Park. We used to love to go to the huge park - to walk around, tour the museums, ride bikes - and play frisbee, touch football, tennis, softball and also Rugby. It's what - 50 blocks long?

http://www.sfgate.com/neighborhoods/sf/goldengatepark/

And how many San Franciscans remember Fleishhacker Pool, billed as the largest in the world? Over a quarter of a mile long.

I can remember as kids in the mid-50's - swimming there (really more like wading?) - and thinking - this is really, really big.

Now it's a parking lot and an abandoned building? http://www.terrastories.com/bearings/fleishhacker-pool-san-francisco

http://tinyurl.com/cm4al4k

"My Bad: Guess the Zoo moved years ago?"

The zoo didn't move - it was never in Golden Gate Park. It was built in the early 1930's where it is now.

The OP is going NOW - not 50 years ago so references to Fleischacker Pool are helpful how?

FirsttimertoCA: If you go to Muir Woods - go early because parking can get difficult. It is great for families because there are boardwalk trails so you can use a stroller.

Oh - they had some animals in Golden Gate Park at one time - close to the De Young Museum. Alligators, etc.

And if you appreciate US history - read about FleisHHacker Pool.

Thank you all so much - I really appreciate your help! I had no idea parking could be up to $60 per night...that's insane! Very good to know things like this ahead of time...that would have been an ugly surprise!

The Columbus Motor Inn near Fisherman's Wharf has free parking.

http://www.columbusmotorinn.com

tom -- the alligator is still there. It is in the Academy of Science. But even you wouldn't confuse the Academy/Aquarium w/ a zoo if you had ever been there.

Have been to the SF Zoo - years ago - and the zookeeper told us that the young male Tiger in with the 3 male lions was not bothered one bit by the Lions.

As for a nice area with free parking - try down by the Marina (also see Chestnut Street and the Palace of Fine Arts http://www.chestnutshop.com/ ) - and this is one of the nicer places - the Chelsea Inn. http://www.chelseamotorinn.com/ There are others - which are cheaper - with a bit more noise - so you can decide for yourself.

Just read the posts again - and Sondoc has good advice for trying the websites for getting real deals.

Also - if you do go over the Golden Gate Bridge - to Muir Woods - if it's a clear day - drive up to the top of Mt. Tam (Tampalpais) for a super view of the Bay Area. http://www.parks.ca.gov/?page_id=471

We used to love to play frisbee in the park up there.

If you don't want to go all the way to SF & are visiting the UC Berkeley campus, you can go to Lawrence Hall of Science. Your 3 year old will enjoy it, there are stunning views of the Ba y Area. On the road up the hill from the campus to LHS, UC Botanical Gardens is worth a stop. On past LHS, is Tilden Regional Park. It has a farm, one of my children's favorite places to visit when they were little. There is also a vintage merry go round worthy of a ride (also a good one in Golden Gate Park). At the other end of Tilden is a train that goes through the Berkeley Hills. All of these make for a very fun day with a little one.

Another trip that is worth doing is visiting the Chabot Science Center in the Oakland Hills, followed by ice cream at the local favorite, Fenton's ice cream parlor.

In Fremont itself, is Ardenwood Farm. Check out their website for weekend events that your child might enjoy. Btw, the Exploratorium in SF is definitely age appropriate for a 3 year old, as it is for my 26 year old!

Just get a stroller and walk. SF is great town for walking. You won't run out of things to see or people to people watch. Google Walking tours SF and you will find a bunch of free audio tours that are great. I love to walk in SF. Day or night. Never boring.

For parking in SF, the Sutter-Stockton St. garage may be the best bet; it's one block from Union Square. Parking from 6 p.m. to 9 a.m. is only $1 per hour.

http://www.sfmta.com/cms/pgar/Sutter-StocktonGarageRates.htm

We live about 45 min south of GG Park and STILL go there at least once a month. When our kids were little we were there about every weekend. There's a nice kid's playground with a beautiful caurosel (sp?) that your 3 year old would love. The Academy of Science is rather newly re-built and has lots for a three year old. Holiday stuff in the main entry. The bison are still around in the paddock by the windmill. Ocean Beach is right there (could be very cold in December but often decent days still). SF Zoo is also not too far away, but probably too much to do both with a little one in one day. Bet you and your child will enjoy GG Park. Go!

love, Love, LOVE Fenton's ice cream!

Are there any areas we should steer clear of, especially if I am out alone with our son? (i.e. not safe, sketchy characters, rough neighbourhoods). I am looking at hotels in either Berkeley or Oakland instead of SF (to save money - I found a few places with free parking, complimentary breakfast & free wi-fi), but I think Oakland sounds a little rundown and maybe not as safe as other areas may be? Am I being over paranoid? Do you have any suggestions? While we are looking for a budget friendly trip, I can't sacrifice safety! I also thought since the parking is free at some of the hotels (during your stay) we could probably take transit into downtown SF so we wouldn't have to pay for parking while over there. I assume there must be a bus or train line that goes across the bay from the Berkeley side?

If looking at Oakland and Berkeley, you might as well look at the motels on the beach front in San Francisco. There are some close to the N-Judah streetcar, and some close to the L-Taraval streetcar (and opposite the SF Zoo)if you decide not to drive into town.

Emeryville is right at the Bay Bridge on the East Bay side. There are good family hotels there, and chain restaurants and higher end shops.

We like the Hilton Garden Inn. Usually has breakfast included, free parking and wi-fi. A good deal.

If the Oakland hotels you are looking at are near the airport, best to avoid them. It's not a nice area.

Emeryville is fine, as are the motels near the beach in San Francisco -- if the savings are significant.

Emeryville or the SF beach would absolutely be fine and big money savers. Oakland would not be fine.

But another possibility could be south of SF near SFO. Milbrae, and other areas. For instance this one is a block from Millbrae BART station. http://www.dylansfo.com/

SFO is a pretty busy place...wouldn't it be really loud at the hotels in that area with all the airport (plane) traffic? I originally steered clear of the SFO area for that reason, assuming we'd hear the planes all day & night. With a 3 yr old who needs his sleep and a hubby that needs some study time, (yes, he has to study while on vacation - boooo) I'm concerned about the noise level. Has anyone stayed in this area? Is this a legitimate concern?

I had booked a hotel in Oakland - sounded great 'on paper' & had nice pics. I Google Street-mapped it, and yikes! Sooo sketchy & inappropriate - cancelled that booking asap!

I think I'll check out the SF beach area as suggested. That sounds nice. Hopefully threre's some good deals!

This may be a stupid question, but can you bring a (jogging style/larger) stroller on a streetcar? I am assuming no, but...maybe? I don't really want to travel with it, but I can't expect the l'il one to hold out all day if we're walking around and there's only so many back & shoulder rides parents can provide before wanting a stroller ride themselves

janisj, I sure like the look of the Dylan! (and their breakfast sounds pretty yummy!)

Janis, I'm just wondering if you've seen the Dylan - I'd not heard of it until this thread.

Firsttimer, I live nearby, and will drive by on my way home tonight and let you know what I think!