Just got back...not a comprehensive list but wanted to share a few places I loved.
Restaurante Los Pacos: Really, really delicious moles. We did not receive the mole sampler as noted in the Lonely Planet book, just chips and 3 delicious hot sauces. My friends ordered mole combos (negro, colorado, amarillo, verde) and I had the enmoladas which came with negro. Unbelievable--the richest, most complex mole I've ever tasted.
El Baresito: this is mainly a bar, but they give "free snacks" with drinks. What you get is totally homey comfort food which seems to just keep coming the longer you sit there. We had peanuts covered in chili powder and lime, small bowls of caldo, jicama with chili sauce, chicken tacos...everything tasted like small eats you'd get in someone's home. Very friendly staff.
Tacos Alvaro: crazy, funny cook, possibly owner? We had lengua and al pastor tacos here...so fresh, with some really great hot sauces.
La Biznaga: Slightly more upscale. Really interesting moles made from guava or berries, great fish, tons more interesting options. A rich 4-cheese tortilla soup made a great starter. Staff was also very polite here, space was beautiful. http://www.labiznaga.org/menu1.htm
20 de Noviembre mercado: well, everything was good here, and dirt cheap. But I wanted to especially note that the tamales at Alejandra's were AMAZING, and the first fruit juice stand you encounter when entering from 20 de Noviembre is excellent as well, with some really unique options (ordered a mixed beet juice by accident...didn't know the word for beets).
Mayordomo: obvious, but might as well mention. This chocolate shop was worthy of a daily visit. I have to say I was really impressed with chocolate con agua, it is lighter with a unique flavor. But it's definitely a bit more yummy with milk. Also a biiig fan of choco mio, the cold version, which tastes way better than Quik but appears to be essentially the same thing :). I also loved how they were constantly passing around samples of the frothy choco mio to anyone in the store.