Neal, visited CA early last year, and as far as breweries go saw San Diego, San Francisco and the surrounding area. Each of the brewery websites will mention if you need to book in advance. And it might be worth checking them out on facebook, a lot of them post info regularly. Green Flash was the only one we booked early based on availabilities on the website, and Stone was the only other one that had limited tour sizes. We turned up to find that the next available tour slot was in a few hours, but they have a really great bistro with a massive bottle list to keep you busy while you wait. Some have tours, some have taprooms/bistros, some have both. Often for $5 you get a tour and a few tasters at the end.
Lost Abbey in SD was one of my favourites. They don’t do tours, but their tasting room was one of the best. Alesmith, Green Flash, Stone, White Labs and Ballast Point are all worth a look in the greater SD area.
North of SF, Moylans, Lagunitas, Russian River and Bear Rebublic are all worth the trip. They all have bistros and taprooms(not sure about Lagunitas, we arrived on a public holiday, so they only had tours of the brewhouse, but that did include tasters). And yes Russian River is well worth the hype. Didn’t go to any of the breweries in SF city, but as jaypes says Monks Kettle is awesome. Massive bottle list and good food but very small and very crowded at peak times. City Beer is another bar/bottle shop worth a visit. There's bar in both SD and SF called Toronado. Didn't make it there, but it was frequently recommended.
You didn’t mention when exactly you’re going to be there. If you’re there in February, then there are a lot of good events at the SF beer week
http://www.sfbeerweek.org/ and you would be there in time for the annual release of Pliny the Younger from RRBC
http://russianriverbrewing.com/brews/pliny-the-younger/ As zappa mentions, a lot of supermarkets have good craft beer bottle selections. Especially somewhere like Wholefoods.
