There's an Air and Space museum in Balboa Park. They have a rarity, a Lockheed A-12, precursor to the SR-71, there. It's quite a good museum. 

The USS Enterprise is a must-see, as most folks won't get to see the inside of a carrier.

My wife grew up in the area, so we've seen literally everything else people have already mentioned and they're all good. I would recommend getting to what you want to see early on a weekend, as many tourist destinations are mobbed by mid-day. If you're willing to drive a little ways north, La Jolla (pronounced "La-hoya") has many restaurants, walking paths down to the beach and tidal pools, where you very well might meet some very rude sea lions.

Above La Jolla is Mr. Soledad Veterans Memorial. It's one of the best veterans memorials I've been to in the US.  The view from above the memorial is quite good, overlooking the memorial and the Pacific Ocean. 

If you're interested in sea life, there's the Scripps Aquarium in La Jolla as well.