Heading to San Francisco

Any recommendations as to which are the two best breweries in the San Francisco area?

21st amendment
San Francisco Brewery
Wunder Brewing Co.
Pizza Orgasmica and Brewing Co
Thirsty Bear Brewing Co.

Just enough time to go to two breweries.

Circle C Brewer

21A and Thirsty Bear are only a 10 minute walk apart. I was there in January and visited them both in the same night so keep that in mind.

Considering they're the only 2 on your list I visited, I'd recommend them. The 21A is just plain awesome, but I had a great time at Thirsty Bear too. It's a bit more formal than the 21A, but their food is great (Spanish tapas style) and their beer is all organic and really good.