In addition to what is mentioned here, here are some smaller breweries and few other places you may want to consider:
1. Lightning (Poway): makes a great Pilsner, and is currently brewing a more traditional German lager which should be ready in June. Also has some fine barrel aged stuff. Porter is great as well.
2. New English Brewing: Recently opened their tasting room near the Coaster station in Sorrento Valley. More English style beers - they have a 4.5% ABV, session IPA (most San Diegans will scream in horror
), as well as a really great ESB and Brown Ale.
3. Rough Draft (in Miramar, close to Alesmith etc): Haven't tasted their beers yet, but have heard really things about the IPAs. Also opened recently.
4. Monkey's Paw (near Downtown): Again - recently opened, haven't tasted, but heard good things. They also carry other local beers on tap and their food is very good as well.
5. Alpine (in Alpine, ~30min drive from SD): Cool little tasting room and brewpub (great ribs and onion rings). If you like IPAs, don't miss the Nelson (rye-IPA made with Sauvignon hops), and Duet.
For brewpubs and beer-focused restaurants:
Lots of places along the 30th Ave:
1. Tiger! Tiger! Great selection of beers, nice atmosphere. Farm-to-table dining (food is delicious but pricey)
2. Crazee Burger: Around the corner from Tiger, they carry some esoteric stuff like Ostrich/Kangaroo/Alligator burger. Decent beer selection.
3. Toronado - always seem to have a great selection of IPAs from all over. Last Sunday they had Pliny and 90min!
4. Ritual Tavern
5. Whistlestop
6. Hamilton's Tavern
In other areas of town:
1. O'Brien's: already mentioned by someone. Beer selection is awesome, food is good as well. Also a lot of Asian restaurants around, if you want to try some authentic ethnic food.
2. The Local habit (Hillcrest): Usually has 10-12 local craft beers on tap. Farm-to-table dining.
3. George's at the Cove Ocean Terrace (La Jolla): Rooftop dining with some of the finest views. Very decent selection of beers on tap as well. Don't miss this.
Have fun here!