OK, so there are lots of good places in the Mission in the City, natch. Nonetheless, La Costena in Mountain View (corner of Old Middlefield & Rengstorff) is still the best in the (known) universe! Especially the pollo en mole, the salsas. They'll be opening a sit-down-and-eat outlet this month nearby, called Burrito Real, up Rengstorff at Middlefield.
San Francisco Bay Area, CA