Maudies: Awesome Breakfast : Pete's tantalizing tacos - eggs, potato and cheese with diced serranos (seeds in!). Depending on your luck with the seeds, you will have varying levels of cornholio en fuego.
El Gallo: South Austin institution. I was raised on it, so there's no better "comfort" enchilada; not necessarily the best, but reliable.
La Fuentes off of S. Congress: lower-rent version of El Gallo; solid old-style Tex-Mex, not sure if it's still there as I haven't been by in a while. Kind of hidden from Congress.
Rosie's: very much in the same vain as El Gallo and La Fuentes. Good South Austin comfort food.
Little Mexico: solid family Tex-Mex, run by Mex-Texans. Maybe even a step up in quality from the El Gallo school. Had a great relleno there once, but I have to be in a certain mood for relleno.
Mexico Tipico: (gone?) always liked the fajitas with the potatoes - some kind of old country regional thing.
La Michoacan: my regular breakfast stop on the way to work. As orngbld said, much more old country style, complete with a TV always on the Spanish stations /soccer games. 2 chorizo/egg/cheese and a Jarritos pina will set your mind right.
Arandas/Arandinas: local chain; many locations to serve you...some people say it requires to "convert" yourself to Jalisco-style, but I can appreciate it and still go back to my El Gallo later. I like the triple-tacos-in-foil thing, queso blanco, and the preponderance of extra grease. No secrets with these folks.
Taco trailers on S. Congress/Riverside/E. Austin, etc. : wherever you find ubiquitous #s of hispanics laborers, you find these roadside kitchens. Some are more established/developed than others. Some you might not even be able to tell they sell tacos unless until you get up to the window. A large percentage of them are unknown treasures.
Often you'll get fresh-made tacos and sometimes even fresh homeade tortillas (corn and flour). Maybe even white cheese, depending on the regional roots of the proprietors.
For the inexperienced, it can be hit-or-miss, but i've found enough good ones that I usually don't mind rolling the dice on an untried trailer. Some of the best al pastor in these parts can be found at taco trailers. Often the only place to get a decent meal after last call, as many of them are open very late or even round-the-clock to serve the large proportion of patrons who work nights or odd hours. Not unheard of to hit one at 2:30 in the morning and have to wait in line.
R.I.P. : Tex-Mex BBQ at S. First and Oltorf (drive-thru joint): Food was great and cheap - how could you not love the idea of brisket tacos with borracho beans and the best homeade potato salad you'll ever have? Ahead of their time, perhaps - or forgotten tradition? I could never decide. Sad that they didn't make it.
Margaritas: hard for me to judge. I always add a floater of Dom Silver, so that tends to be a great equalizer...