I think that right now my absolute favorite place is Mike Hess. Go now while the brewery is still nano (they're building a new big brewery in a new location). The atmosphere in that little storage space brewery is fantastic. The beer is great and the people that hang out there could not be friendlier. Say hi to Steph (she used to work for Rogue).
2nd favorite place is Societe, simply because The Pupil is my absolute favorite beer coming out of San Diego. One of the absolute best IPAs I have ever had. Great tasting room, the only thing that separates you from the brewery is the bar. Very friendly folks there too, like Steven the tasting room manager. My advice, go around 3-4PM and you might get to see the brewers at work and get some food from one of the lunch trucks.
3rd favorite would be Alesmith, I liked it better before the new bigger tasting room but still a great spot. I used to work a few blocks away. Speedway Stout is one of my favorite beers, my friends have had kegs of Speedway going in their kegerator for at least 5 years nonstop.
Ballast Point, massive selection of great beers and they usually have some interesting barrel aged varieties. I personally don't like the atmosphere as much here because it seems to be a focus for beer bus tours and the place is usually jam packed with drunks. I prefer the Ballast Point tasting room at Home Brew Mart, same great beer and a more intimate atmosphere.
Stone, you have to visit just because, it's worth a pilgrimage.
I don't find anything about Karl Strauss appealing but that's just me.
Pizza Port is awesome, I have really only been to the San Clemente location recently but they make killer pizza and the Shark Bite Red is always a great go to.
There's also Coronado and Green Flash, neither of which I managed to drop into on my last trip home so I don't know about the atmosphere these days.