This is not a great time to visit the DF if you are targetting specific restaurants -- we had wanted to try Aquila Y Sol and Izote, both were closed, and D.O. was only open for lunch (as as janeabby posted, after a huge breakfast we usually just snacked at lunch). One great lunch was at Tostadas Coyoacan in the market there, we followed Jim Johnston's guidebook and enjoyed his perspective (but it's already out of date on a few instances).
Our best meal was at Pujol. We took the advice on this board and got the tasting menu, but asked them to give us some substitutions on my dinner so that we could both taste more things. They misunderstood and gave us two entirely different tasting menus, which was even better. They were also extremely gracious when I asked to have our table moved away from the smoker next to us. There were smokers throughout the one-room space but at least it wasn't being blown directly in our faces. The website (they are on OpenTable) shows the menu, in Spanish, although obviously many of the dishes we had were different from the sample shown.
They are a big fan of foams, and in general I thought this was wonderful. Here are some notes: Amuse bouche: liquid quesadilla with oaxaca cheese and foamed tortilla and (?) nopales? Escargot with cilantro potatoes - made us sorry we weren't having the full portions, we wanted more. Cactus salad: ground tortilla, strips of nopales, and oaxaca cheese. Squash blossom cappucino - wonderful. Dorado on a green sauce & grilled sole with frijoles sauce under: both wonderful. Beef with foam and 2 sauces: artichoke lemon and (maybe) asparagus cream?Eh.
We had breakfast at Maque in Condesa (there are several branches in different areas) and while the baked goods were spectacular (we carried a bunch home on the plane, even a dayold they were delicious), the eggs were only okay.