SD Zoo
Legoland (can't believe it's not on the list already!)
Disneyland
Long Beach Aquarium
Drive up the coast PCH/101 towards Oxnard, swing by the military missle & aircraft display at the small air base just south of Oxnard.
Cut back to the interior and head up the 99 to Sequais and the into Yosemite.
There is a great book for hiking Sequoais and Yosemite with kids. Here it is: http://www.amazon.com/Short-Hikes-Yosemite-Sequoia-Canyon/dp/0899971326
I've used this book a lot, it's kid rated!