I was just in San Diego for four days (Sat through Tuesday), from New York. I was fortunate in that I had pretty much all four days to drink beer wherever I wanted. Here is what I did in terms of breweries:
Sunday:
Stone (Escondido) - Awesome place, bunch of menu items, finally tried Pliny (the Elder) which they had on tap. Tour was OK - the tour guide was annoying. Building is spectacular, as are the back garden and patios. About 40 minutes from La Jolla.
Monday:
1. Callahan's Pub and Brewery (they brew their own beer, though it wasn't spectacular). Definitely better brewpubs to hit (Rock Bottom, even Gordon Biersch)
2. Karl Strauss (Sorrento Mesa location): They don't offer tours of their brewery on Santa Fe Street, so I went to this location. Cool Japanese gardens feel. Crowded but sat at bar and got food fast. I enjoyed the beer. They just won a gold at World Beer Cup for Red Trolley
3. Ballast Point Brewery: Cool operation, great tour guide. Also shows their distillery operation which is running now (not tasting of the gin, rum, whisky though). I toured with just three others and we were all beer enthusiasts so we just talked the SD and Cali beer scene the whole time. They had a ton on tap and some really creative stuff. I snapped a pic of their tap selection for tasting:
Also, the tour guide raved about Alpine Beer Company. He said that a bunch of Ballast employees would go there and drink before going to work at Ballast. His opinion is that Alpine was doing the best beers in San Diego right now. I decided to hit up Alpine on Tuesday (see below).
Tuesday:
1. Pizza Port (Carlsbad location): I heard great things about all locations, including Solana Beach, but headed up to Carlsbad b/c it is right near Texas Liquor, which i heard is a great bottle shop. Pizza Port didn't disappoint. Lots of good things on tap including guest beers. About 40 beers on tap. Really unique place, at least for anyone from the East Coast. While I was at Pizza Port, the brewers there also raved about Apline Beer. Said best IPAs on the West Coast now.
2. Alpine Beer Co: Long drive from Carlsbad, but worth it. In really high demand now. They limit the number of bottles you can buy to 4 of each kind (but said they might bump that down to 2). Great beers, lot of hoppy offerings, as expected. Small operation. Operates a pub at an adjacent location, so grabbed food there which was good.
I wanted to hit up Green Flash and Hess but didn't get the chance unfortunately. If you want any info about the particular beers on tap at any of these locations, I can provide more details.
Here is an article about the San Diego breweries that won medals at the world beer cup lst weekend