The Burrito Tour guys have inspired me to post my own thoughts about burritos in the Mission.
First, some credentials: I've lived in the Mission for 5 years now, and have been eating burritos here for perhaps 12 years on and off. I eat in a taqueria about 2-3 times per week (seemingly whether I want to or not!) for either lunch, dinner or a snack.
Authenticity: according to my sources (several friends who grew up in Mexico City), there is no such thing as an "authentic burrito" in any Mission taqueria. Tacos, yes. Burritos no. Burritos as we know them appear to be a San Francisco or at least California invention.
El Farolito (the one on 24th and Mission) is open later than just about any taqueria around, which makes it a good after-bar spot. In fact there are often long lines at around 2am. I first went to Farolito a long time ago, when the Mission seemed much more dangerous than it does now. Going there at 2am seemed quite adventurous if not fool hardy. The place hasnt changed at all, but seems a bit safer, and they do have a guard on weekends. The vegetarian burrito here is quite good, with excellent bean flavor and nice amounts of fresh avocado. Farolito also has the best salsa verde around, with plenty of avocado in that too! Its informal dont hesitate to go behind the counter to take your own salsa. I even grab a cup, fill it with ice (from behind the counter again) and take some water from the sink for myself, as Ive seen others do. They dont seem to mind, and actually appreciate not being bothered when the line is stretching out the door. The al pastor is highly recommended here, and they have sesos (brains) and tongue on the menu as well. Grilled chicken is a recent addition to the menu, but they tend to run out as the night wears on.
El Toro and Pancho Villa are under the same ownership, but I like El Toro (17th and Valencia) better. In fact, its my favorite taqueria in the mission (though prices have gone up a bit lately). Both have excellent salsas, a free salsa bar, and interesting specialties like beef with cactus, grilled vegetables, and several kinds of shrimp (grilled to order and available on tacos, burritos, or plates). Pancho Villa (16th between Mission and Valencia) is the premiere taqueria in the Mission in my mind at least, because its the largest (or was until recently), serves the most people per hour (undoubtedly), and manages to have excellent food nonetheless. Its open til midnight.
There are two San Jose Taquerias across the street from each other (between 24th and 25th on Mission). I dont really understand the point of this, but they are a bit different. The good one (in my opinion) is the one on the west side of the street. It has better atmosphere, and is airier and more open. They have the best (spiciest) pollo assado, and very good al pastor. For a vegetarian burrito, you'll do better across the street at Farolito.
El Castillito (17th and Mission) has excellent pollo assado and al pastor as well, but its a bit sketchy: the stretch of Mission between 16th and 18th is probably the worst part of the neighborhood. Not for the faint of heart, even nowadays.
Papalote Mexican Grill (23rd at Valencia). Its trying to be trendier and a bit fancier than other places, but it is quite good. It offers a little more service than other places (order at the counter, but then they bring you your food), is a slight bit more expensive, but is still worth a try (if not a special trip). They have a sign offering their special salsa recipe for $100,000, and while its not THAT good, it is really very good. If anyone can figure out whats in it let me know.
La Corneta Taqueria (Mission near 23rd) is the new kid on the block. Its about as big as Pancho Villa, but newer and a bit fancier. Very clean, good quality, friendly help, but not quite up to the level of my favorites. A pleasant place to relax and talk, though, if you want to get away from the hustle and bustle of the busiest places.
Can-Cun is always winning awards for their vegetarian burritos, but I don't like the place much (the main place, that is, on Mission and 18th. I haven't tried the others). I find they're usually too salty for my taste, nothing else to really recommend them, except that they heat the burritos on a grill (which some people love Farolito also does this). Also, the place is a hangout for gang members, who sometimes have loud aggressive arguments while the staff either ignore what's going on, or actively cower.
La Cumbre (Valencia at 16th) also continues to get awards for some reason, but I dont know any local Missionites who actually go there. There seems to be nothing particularly special or good about it, making its continued award-winning seem odd.
Altena (Valencia at 22nd) is OK in general, I suppose, but I cant get over the fact that they will use cheese syrup on your nachos if you dont specify that you want actual real queso blanco. That ruins it for me right there!
Mariachi's (Valencia at 16th) tries to be fancy, has mango salsa, etc. and does as good a job as they can manage, but since they get so much less traffic than other taquerias in the neighborhood the ingredients just arent as fresh as they could be. And I hate that caricature cutout of a mariachi singer they keep in front of the place!
La Taqueria (Mission at 24th) is also often cited as a great place, but I just dont see it. Ill defer to the Burrito Tours reviews on this one.