See the Zoo and Balboa Park, which it is in (just...walk around and it's awesomely fun). Coronado is cool: the hotel at teatime is especially nice (grrl thing). The Old Globe has great plays, and the Gaslamp district is nice to walk around in (so is Hillcrest, the major gay area).
I'll be there next week en route to MX. Whale watching (which I've done in NF) is iffy. Sometimes you don't see anything.
Enjoy. I always do. I stayed at the 500 West, which I highly recommend.