Make sure you go to:
Stone, at least for the building/tour. Beautiful.
If you have a car, goto Alpine Brewing Company to their pub! It is far, about 45min each way, but totally worth it!!!!! AWESOME beer. My favorites here. IPA Duet is amazing. Bad boy, Pure Hoppiness, jesus, my IPA mecca. If you are an IPA guy, go HERE. Food is also great.
La Jolla Brewing Company. They have a new brewer, who brewed with Vinnie Cilurzo. Fantastic WC IPA, and a great DIPA to boot. Food is fantastic here also.
Alesmith. You can't come to this town and not stop by Alesmith for a tasting. It isn't a brew pub, but some of the best beers around.
Ballast Point. I live less than 2 miles from here, and there is always something new on tap. Won best small micro-brew and IPA at World Beer Cup 2010. Home of the India Pale Lager (no longer on tap), and an amazing Session IPA that was 3.5%. Also not on tap. Just recently had a Chiptole Choco Porter (I didn't like it, but others love it! Then again it was 11am in the morning and I was hungover and buying brewing supplies. It is also a home brew store) Goto the home on Linda Vista Rd. Stupid not to come to this city and go here. Also not a brew pub.
San Diego Brewing Company has decent microbrews, but have a great selection of other local microbrews and microbrews US wide. GREAT food BTW.
As for beerpubs, there are some great ones, I love Small Bar and Hamiltons. Hamiltons has a hop sausauge, but I think it sucks. Not enough hop flavor. I had a Pliny the Elder with it expecting a double slam, but all I got was the Pliny. The grilled cheese sandwiches here are the best in the city though
O'Brains is also awesome. I live/work/band practice right by this place. I am here all the time and it is dog friendly. The owner is good friends with the owner of Alpine, so they always have Alpine on tap if you can't make it out to the mecca. FOOD IS AWESOME. They sometimes have an O'Brians IPA which is brewed by Alpine and also fantastic.
Hope this helps. Cheers