I hate to stray too far from the original Atlas Cafe focus of this post, but I do live in the area and have a handful of recommendations (most of which are somewhat shy on ambiance, but certainly made up for by high quality and reasonable prices):
El Rinconcito Cubano: incredible ropa vieja in a lively but modest, byob setting. I dream about this stuff. 3248 W. Fullerton
El Pacifico: not byob, but the very passable margaritas are only $3.95. This is a wonderful family-run place with excellent, rich dishes for vegetarians and meat-lovers alike (great chiles rellenos). Plus they always seem to be open (we had an excellent, hangover-busting breakfast last New Year's Day morning): 3534 W Fullerton (be careful, b/c they generally include the tip in the tab; this is clearly indicated on their menu).
And of course people have written at length about the wonderful taquerias and cafeteria-style offerings in the area, but the following deserve special mention:
Cafe con Leche
Burrito Joint
Tropicuba
Guanajuato grocery
Carnitas Paisa
Also, there seems to be a new place on Fullerton just west of Kimball (south side of street) with a sign that simply reads, "Cafeteria." The food looks great, but I haven't had a chance to try it so can't vouch for its quality.
Happy hunting . . .