Eduardo's: Two excellent spicy chicken border burritos on recent trips. These guys may make my favorite burrito on the west side. The key is the way they start by grilling the cheese with the tortilla, which helps ensure proper heat and melting. The drawbacks are the white rice, no whole pintos or refritos (i.e., only whole black beans) and no meat choices besides steak or chicken. Still, the meats they serve are tender and well marinated. If you're looking for carne or pollo asada, and don't mind black beans, this is the place.
Tacomiendo: Many thanks to PaulF and Dommy! for turning me onto this place. I was impressed with the orange rice and choice of beans (i.e., whole black and pinto, as well as refried). I was also pleased that guac, and sour cream come standard on burritos. I appreciated the choice of agua fresca besides tamarind and horchata, though I'm still looking for a place that has strawberry on a regular basis. Unfortunately, my burrito was rather poorly constructed, and quickly fell apart (PaulF warned me about this). Also annoying was the poor dispersion of ingredients -- guac and sour cream were confined to one end. Finally, my al pastor was a little on the dry side, and my friend's carne asada seemed to lack flavor. When I go back, I'll give some of the plates a shot.
Tacos Por Favor: Before I found Eduardo's, this was my go-to place because of the whole beans and multiple meat choices. Unfortunately, my most recent al pastor burrito was a bit of a letdown. The meat had a funny taste -- not so much rotten as strangely spiced. Also, I noticed they tend to skimp on the guac and sour cream, which you have to order separately.
Taco Plus: I rarely see this place mentioned but they're right up there with Eduardo's for my favorite burrito on the west side. Fillings and set-up are similar to Tacomiendo, though no refried beans or agua frescas. On back-to-back trips, the al pastor was tasty -- a nice balance of crisp and juicy. Best of all, the burrito was well constructed, esp. the second trip, with good proportions and dispersion of fillings. My main complaints are that they don't seem to serve refried beans, and the tortillas are a tad too thick (also a problem at Tacomiendo). Still, if you're a Bay Area expat looking for a Mission style burrito, Taco Plus is the closest I've found so far...