my pet-pev is you need a bit more to go on for a thread like these, bay area is big (tagging SF, means only SF or beyond?). Simply naming a place is pretty pointless. Drive by replies with no useable info just make noise.
My recommendations have since closed, la costania in mountain view on rengstroff. Was the guinness book holder for longest burrito. fresh meats and line style so you can pick all the parts as you move through the line. We have so many places in the bay area, maybe we will get some useful info in this thread.
I need a new place, chavez markets seem to be ok, but can be hit or miss, several locations through out the bay area. Not all have a eatery so you need to verify online.