Very timely thread, as I've just gotten back from a recent stint in Chicago and could dust up on some of my favorite old places, as well as a couple new ones.
Topolombompo is fantastic. I'm a huge fan of discovering a lot of varieties of Mexican food -- it's one thing I really got into down here in Texas -- and I can assure you that Topo does it absolutely as well as any place in Texas (that is, for authentic Mexican food, not Tex-Mex).
On the other hand, Frontera Grill, which is more casual, is also fantastic. Their brunch, in particular, on Saturday is knockout. I was really impressed with the level of cuisine at both places. Rick Bayless rocks.
Everest has been a family favorite for many, many years. They have a tremendous young sommellier and a really top-notch wine list.
On the pizza front, I went back to Gino's East just last month, and I have to say that they're not operating at the same high level they used to. Don't get me wrong -- I have a huge soft spot for Gino's -- the sausage is still fantastic, and the crust is the best around. But there's one major problem: Gino's isn't using enough cheese these days. I talked to a waiter about it. He said they went to a new proportion a few years back and cut back on the cheese. It wasn't oozing out of the pizza like it should. Very sad. But maybe you can ask for extra cheese. At this point, however, I prefer Giordano's or the original Uno.
Anyway, sorry to drag on, but I had to give my take. I love Chicago's restaurant scene, and there have been many excellent suggestions made here. You're going to have a great time.
A couple other places I've heard raves about recently: Brasserie Jo and Les Nomades.