I did a 4 week trip to the US last year in September which included LA and San Francisco. It went with my partner and our two kids aged 10 and 12.
Make sure you grab a San Francisco City Pass (
www.citypass.com/san-francisco). It gives you discounted entry to a range of popular attractions which are all well worth seeing. More importantly it gives you unlimited travel on the Muni, buses, trams and cable cars for 7 days. We used public transport to go everywhere and it was invaluable. You won't want a car in San Francisco as the public transport is great.
We took a San Francisco Urban Tour (
www.theurbansafari.com/tours/sf) which included an Alcatraz Tour in the afternoon. It gives a good overview of all the main sites however you only get 10-20 minutes at each location so it is only really a taster. Don't be put off by the look of the vehicle, the couple that run it are great and it was well worth it.
If you're more adventurous, you can take a day trip out to Yosemite National Park. It is a long day though and is a 5-6 hours drive each way, but was well worth it as the scenery is breath taking. You only get around 3-4 hours in the park though. We went through Incredible Adventures (
www.incadventures.com/trips/yosemite/yosemite1day.php) who run a small group tour of 12 people. Our guide was really knowledgeable and friendly. A two day tour would be better as it goes deeper into the park but you have to balance that with what else there is to do. Despite the long trip our kids really enjoyed it. The whole trip they wanted to see a squirrel and by the end of the day they were over them. If you're not up for a long day trip, try Muir Woods which is closer to San Francisco. There are plenty of tours out there.
My Cousin did a hop-on hop-off tour in San Francisco (
www.bigbustours.com/eng/sanfrancisco/custompage.aspx?id=tour_of_san_francisco&gclid=) and said it was great as they could take their own time at many of the destinations rather than being rushed.
We stayed in Hayes Valley and there are lots of nice cafes and restaurants around there, but not really much else to see. It was a great place to stay though. There was a place called Smitten in a park on the corner of Fell & Octavia that makes icecream fresh on the spot using liquid nitrogen. It was the smoothest, most creamiest icecream I've ever had.
When in LA you will need a car. I don't think we could have managed it without one. I bought car rental and excess insurance through a UK broker for approximately GBP100 (
http://www.questor-insurance.co.uk/). It saved me from paying the inflated $20-$30/day insurance surcharges from the car rental agency. Only issue is that if anything happens to the car you have to pay the rental agency, then claim it form the insurer.
If you only have one day at Disneyland, go to Disney California Adventure. It's a much better park than Disneyland (better rides, more open space). Make sure to see the world of colour show at the end of the night. To get the best view you need to grab tickets which can only be obtained from the Grizzly River Run ride when the park opens. Typically most people head there first to grab a ticket before they run out. You can also pay to have a reserved dinner seating.
Universal studios was really good and you'll need to get there when it opens. It can be done in one day if you do it right. Go straight to the studio tour when you get there as that gets busy quite fast. Once you've done that head down to the lower level and do all of the rides there such as Transformers 3D, Jurassic Park, etc. Next head back up top and do the Simpson's rides and then make your way through the park to the Waterworld Show at the end of the day. Finally go through Universal Citywalk.
I was pretty disappointed with Hollywood but there are a lot of things well worth seeing nearby. Beverley Hills is nice and the Cheese Cake factory on the street behind Rodeo Drive was our best meal of the whole trip. We went to the La Brea tar pits which has a museum full of ice age fossils that have been excavated there. It was really interesting.
Lego Land is worth going to if you love Lego but the rides are pretty tame and aimed at kids under 10. The city scapes made from Lego are pretty cool. It is also a 3 hour drive south of LA. The other other theme parks are much better for rides and entertainment.
On our last day in LA we drove along the coast through long beach. There is a WW2 Battleship USS Iowa moored there which you can go on. Unfortunately we didn't get the time.
EDIT: I did start doing a photo log of our trip but it sort of stopped as I was enjoying myself way too much to be posting lots of photos:
http://www.deathinc.com.au/index.php?topic=15293.0
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