I'm pretty new to the bay area (lived in NYC and Connecticut for past 4 years) but have to recommend Pancho Villa in San Mateo.
I've been trying lots of burrito places since I moved out, and, while I'm no expert in authentic mexican burritos, this place is simply fantastic. The burritos themselves are the highlight, but what makes Pancho Villa so great are the complementary things - 6 or so varieties of fresh salsa that you can help yourself to, roasted jalapenos, lightly pickled carrots and jalapenos, and fabulous jugos frescas - incredibly refreshing drinks made from such things as cantaloupe, watermelon, strawberry, tamarind, etc. A perfect cool off to the heat of the salsas and jalapenos.
As for the burritos, the mole chicken and carne asada have been my favorites, though all I've tried have been very good. The quality of the ingredients is top notch, from the black beans (my choice) to the perfectly cooked rice to the guacamole.
Pancho Villa probably doesn't need my post here, as they tend to be pretty crowded all the time with people from all walks of life.
I know they have one in SF also, but I've only been in San Mateo.