Stone was the biggest letdown of our trip. The only stone beers on tap were arrogant bastard, SSR, levitation, IPA, pale ale, and ruination - all beers I can easily get at my local grocery store. While the food was great, the wait (2 hours) wasn't. Also, the place looks really cool, but feels like a chain restaurant, not a brewpub. Good news, though, if the wait is super-long, Port/Lost Abbey isn't far away and neither is Green Flash.
Ballast Point, Green Flash, and Alpine Brewing Co. were all really awesome, as was a beer bar/pizza place called "Blind Lady" on Adams Ave. Many (most?) breweries are only open Friday and Saturday, so make sure you check before you go. We didn't, and ended up unable to visit Hess and Ale Smith.