Definitely go to Ballast Point. Both locations if you can (Since there's no such place as Ballistic - I assume this is what you meant. Besides, it's my favorite local and also my LHBS). Pizza Port Carlsbad is my favorite of Pizza Port Chain, although the Port/Lost Abbey brewery can be cool too. Might as well go to Stone, it's pretty fancy pantsy. Plus they have daily free brewery tours complete with free samples. Green Flash and Alesmith are cool, both pretty standard production breweries as far as visitation is concerned - great beers though. Alpine is really out of the way and has weird hours, so if you plan on making that trek, make sure you time it correctly.
There's also a buttload of good beer bars in town. Most of them are a short cab ride or medium walk. There is, O'Briens, Hamilton's, Small Bar, Toronado SD, Blind Lady and Live Wire. All have their own charm and great selections. All but Live Wire have food, and good food at that.