I went a year ago, the food was awesome, the beer was great as well.
One place I loved and recommend to everyone I know that goes there is to go to Tom Ham's Lighthouse for the Sunday brunch. If you're at all into seafood it's worth every fucking penny, and if not, the scenery is amazing. I have fantasized about flying back there just for the brunch. The waitress was great about keeping us loaded with champagne for mimosas.
There are a ton of great breweries if you're into beer at all. The Stone Brewery (Escondido location) was fucking amazing, but I am a big fan of their beers. Karl Strauss had a great restaurant as well (Downtown location). The Cioppino was the best ever. I did go to Hodads as well, due to DDD, loved it.
The whole trip was dying and going to food heaven, and this is coming from a New Yorker. The zoo was cool there was just a colossal downpour when we were there. Gaslamp was fun but I was hoping for a bit more in terms of clubs/lounges. It also wasn't baseball season, so we were only able to tour Petco, I would love to attend a game there. The only thing that sucked about the trip was the Giants getting stomped by the Chargers.
I would retire to SD right now if I could.