Here are a few of my favorite things that you might not know about, from south to north:

(1) Of course the San Diego Zoo and Balboa Park, but while there visit (or stay at) the historic Hotel del Coronado and beach, a national historic landmark.
http://www.hoteldel.com/

(2) Walking downtown in Santa Barbara and enjoying the tropical spanish mission ambience. Visit the famous Santa Barbara mission
http://www.santabarbaradowntown.com/
Slightly north of Santa Barbara is the Santa Ynez Valley, which is the southern equivalent to Napa County. Great wineries and restaurants.

(3) Walking the pier in Santa Monica near downtown LA, scene of many movies. Stay in Marina del Rey. Alternately, you can stay and visit Laguna Beach which is more isolated and resort-like with galleries etc., but less "LA-ish". Depending on your interests, many people like walking down Rodeo Drive in Beverly Hills, then driving around the homes there. J. Paul Getty left a massive fortune for his foundation to build an art museum (Getty Museum), it is incredible but book well in advance if you want to go. If you want to see the amusement parks, LA is the place to go (Universal Studios or Disneyland). Warning: traffic in LA is awful, so overnight near the sites you want to see or all your time will be spent driving in traffic.

(4) Stay overnight in the little resort town of Cambria, and then visit Hearst’s Castle at San Simeon, the famous residence of William Randolph Hearst which the Orson Welles movie "Citizen Kane" was about (this is a MUST, will take most of a day)
http://www.cambriachamber.org/
http://www.hearstcastle.org/

If you are going on the actual coast highway (CA 1) then allow a day to Carmel/Monterey. This is beautiful coastline, but very steep and windy, through famous Big Sur.

(5) Stay overnight at an inn or B&B in Carmel, California (Clint Eastwood’s home town) Visit famous Pebble Beach and the famous coastline there. If Carmel is too much $$$, you can opt to stay in a actual victorian B&B in Pacific Grove, which they are famous for. While there, visit Monterey Bay Aquarium which is one of the best in the WORLD. If you arrive before winter is over, you can also visit one of the few sites where the monarch butterflies west of the Rockies migrate to, literally thousands of butterflies hanging in the trees.
http://www.carmelcalifornia.com/
http://www.mbayaq.org/
http://www.93950.com/monarchs.htm

(6) San Francisco has too much to list here! Do make sure to drive over the Golden Gate Bridge to Marin County, drive up the Marin Headlands, through Sausilito and eat at Guaymas or Sam’s on the water in Tiburon. Alternately, you can take a ferry in the bay from SF to Tiburon, the restaurants are right there. If you go north through redwood country, no need to go to Muir Woods. One of the most beautiful beaches in Northern Cal is Stinson Beach, but difficult to get to as it is where Mt. Tamalpais runs down to the ocean.
http://en.wikipedia.org/wiki/Stinson_Beach

(7) Napa County has great wineries and restaurants, some are Michelin rated. Visit Robert Mondavi winery first for an intro, it is the best infrastructured. Mustard’s Grill restaurant nearby is casual elegance, but you absolutely need to book in advance. The town further north of St. Helena also has noted (but pricey) restaurants such as the French Laundry, one of the great restaurants in the USA.
http://www.mustardsgrill.com/

(8) North of San Francisco, the number of people and towns becomes sparse. You may want to overnight in Mendocino if you are going slowly. It is a noted B&B coast town.

(9) North of Menocino really becomes redwood country. The Avenue of the Giants, trees that are over a thousand years old and 200-300 feet tall (the highest in the world). Some trees are wide enough to drive through.
http://www.humboldtredwoods.org/