I'll probably think of more, but my two favorites are:
A Cote: lesser-known grape varieties from all of the world, always something new, huge selection by the glass, lots of flights, knowledgeable staff. If you're a wine nerd, be sure to ask to see the reserve list.
Great China: big selection, low markup, strong in Burgundies, Bordeauxs, and Rhones and domestic Pinots, Cabernets, and Bordeaux-style blends, sometimes great buys in older vintages.
5478 College Ave, Oakland, CA 94618
Great China Restaurant
2115 Kittredge St, Berkeley, CA 94704