Lots of things we love have already been mentioned, but here are a couple I would add. Many of the suggestions could be done after a day of work (or conference)... I love going to the harbor and taking a cruise around the bay. The have 1 & 2 hour trips, lots of fun and they tell you a lot about what you are seeing. If you have some early morning time and are close head over to the little shopping area where the ferry drops you off on Coronado Island - you catch it in the same place as the cruises. There are a couple very good coffee shops with great breakfast treats, and the view of downtown San Diego is wonderful. Same goes in the evening, watching the sun set against the buidlings is truly a sight. A bit further north along the shore is the Star of India - a large sailing vessel (hope it is still there) and they have self guided tours. Right near there is a seafood restaurant, it has 3 different places. One is a fast food counter, there is a moderate priced sit down area and then a higher end fine dining place. We've tried all three and they are wonderful.
Up in Pacific Beach there is a great omlette place, I'm sure the folks in your hotel can tell you about it. Also, in the evening over by the Bahia, Catamaran and one other resort there is a riverboat that runs between the three hotels, has live music and dancing. It is a great time!