San Diego Zoo--heck you might even want to do the Roar and Snore there.

Wild Animal Park(the zoo owns this, I think they call it something else now). We actually liked it better than the zoo, but I don't think we would have if we hadn't spend the $$$ on all the extra things. Like a tour where you can feed the giraffe and rhinos. The tour where the cheetah runs. And there are more.

Seaworld, if you haven't ever been to one of those.

The Grayline LA tours are the best way to see a lot in a short time... you can take a set tour or a Hop on hop off ... they cover everything from the beaches to Hollywood and you don't have to drive or park...

Disneyland, Disneyland's California Adventures, and Knott's Berry Farm are all approximately halfway between San Diego and Los Angeles. The boys might like Medieval Times near Knott's Berry Farm where you have a meal while watching knights joust.

Balboa Park in San Diego has the Air & Space Museum, interactive Reuben H Fleet science museum, and natural history museum (dinosaur bones!) that are fun and educational.

Santa Monica Pier, Train Town in Griffith Park in LA (be sure to check the schedule first), ride bikes along the beach between Venice and Santa Monica (you can rent bikes, and I think you can even rent a tandem if you aren't sure about the 6 1/2 year old on his own). I believe you can see the Space Shuttle at the California Science Center now in Exposition Park, and the Natural History museum there is lovely, with dinosaur fossils etc. and a great kids exploration room. I am partial to Will Rogers State Park, with a wonderful easy hike up the hillside overlooking the ocean and a beautiful patch of grass for a picnic if the weather is good.

La Brea Tar Pits and the Page Museum (fossils)

Museum of Natural History and The Science Center

Griffith Observatory & a Planetarium Show

Los Angeles Zoo (if you don't do San Diego)

Legoland

Petersen Auto Museum

San Diego: My kids love Legoland and SeaWorld. For quick weekend trips, we stayed at West Inn and Suites near Legoland. The kids liked the breakfast buffet and small pool, and I thought the price was right. We've also stayed at the nicer resort hotels and in La Jolla for longer vacation trips. I like the Wild Animal Park and the San Diego Zoo too. The animal park is a little out of the way so we usually stopped there on our way home. We did the behind the scenes tour at the Wild Animal Park which I thought was awesome. We spent one sunday morning going to the massive brunch at the Hotel Del and then rented the big 4 or 6 person bikes and rode about. The kids also liked playing on the beach by the hotel. La Jolla is also pretty cool and has a nice cove.

Los Angeles: Here are a few suggestions for the younger set. In Pasadena: KidSpace by the Rose Bowl, Huntington Museum and Gardens (including a kids oriented water park and a rainforest); at Griffith Park enjoy: LA Zoo, Gene Autry Western Museum, Travel Town (a collection of old trains) and a really cool play park called Shane's Inspiration (fully accessible, public park); on the west side, mid-Wilshire area: La Brea Tar Pits/ Page Museum (love the working scientists exhibit), LACMA, and Petersen Automotive Museum; on the far west side: Santa Monica Pier, several kids play spaces and craft studios, the beaches; south of downtown you'll find the California Science Center which has the Endeavor space shuttle and a great collection of science/nature things to engage the kids. And, of course, the Theme Parks.

Lots more to do as well but that gives you a pretty good start.

The Midway aircraft carrier museum in San Diego.