Hog Island Oyster Company, SF
This is a real gem and true food in the purest and most beautiful sense. This place (more of a bar than a restaurant - it's in the corner of the market, but really nicely decorated with a view of the bay) is at the San Francisco Ferry Building, serving local oysters from their waters just north of the city near Point Reyes (if you visit their oyster farm instead, they will serve you fresh oysters on the beach). The menu is very clean: basically just oysters, clams, wine, and beer (all on tap, BTW - they refuse bottles - yay!!). They barely even use the stove - it's practically a cold bar where they shuck oysters in front of you and pour beer from tap. Paradise.
The oysters were very, very fresh - so much that I didn't even really put anything on them, choosing to eat them straight instead. A wide variety is available: Sweetwaters, Atlantics, Kumamotos, and French Hogs. The steamed Manila Clams were perhaps even better (which really says something) - the white wine and butter were heavenly (seriously - once you taste it, you will say, "wow"). Skip the clam chowder though if you get the steamed clams. Although the clam chowder isn't bad (interestingly, they include the shells), the steamed clams are better, and they basically use the same clams.
Try to go on Mondays from 4-6 PM - it's happy hour ($1 oysters and $2 beers). But beware too - they close early (8PM), and you may have to wait a bit as it's a small place.