from here
La Jolla Cove - walking around there, and lots of restaurants too.
Downtown / Gaslamp quarter is awesome. Tons of bars and restaurants.
Seaport Village - downtown on the bay is nice, kinda touristy.
Midway Aircraft Carrier museum - Very cool, down a mile from Seaport Village
Cruise around the bay. all the charters are around down by the Midway.
And of course the Zoo / Sea World / LegoLand. Try the Safari Park, it's part of the Zoo.
Old Town is great for some Mexican culture and great mex food.
The Brigantine does have great fish tacos, but IMHO the best are at South Beach Bar and Grill in OB at the end of Newport Ave. They also have a great selection of beers, and represent San Diego's amazing beer market quite well. Also, Hodad's hamburger joint is right there, one of the best burgers around.
That's another thing you could do, go beer tasting!
Stone, Ballast Point, Port Brewing/Lost Abbey, Green Flash, Alesmith, Karl Strauss, etc...
Ballast Point just opened their new brewery/HQ in Miramar, it's amazing.