It's not in San Diego proper, but a short drive east is Alpine. Best lineup I tried all week. And I was there on Taco Tuesdays. Bonus.
Lost Abbey if you haven't had their beers before. The new Pizza Port was good. Toronado had a good selection, and I didn't feel like I was about to get knifed like I do in SF. I thought Ballast Point was a bit hit-or-miss. Coronado had a good 3.8% Scottish when I was getting tired of hops.
Anyway, you pretty much can't swing a dead cat and not hit good beer in San Diego. Alpine was my unexpected find for the week. I think Duet and Ugly were my two favorites, but I would have had several of any of them.