Well, there are over 40 now and it's a big county, so depending on where you'll be staying and what you'll be doing,and what you like, it just depends. Toronado and Hamiltons will have lots and lots of different San Diego as well as California beers.
You mentioned your availability in Boulder so I'm sure you have had Ballast Point and Green Flash. Stone is on your list, its a neat place to visit and they are also great in that they will have several taps of other micros that they think are great.
Alpine is awesome but out of the way a bit. Alesmith should be visited. If you find yourself in Coronado you should check out the namesake brewery there. Pizza Port in Ocean Beach is very good and you can then walk to Newport Pizza and the Harp which are bars with some great taps.