Biz is going to recommend Alinea and Charlie Trotter's.
You were talking about Indian food the other day, Jane; there's a whole shitload of Indian places, all good from what I've been able to determine, up and down Devon Avenue.
Haven't been to Trotters.
We've been going to Chicago quite a bit recently (and going again mid-September), so have a wide range of suggestions. Actually did a one week foodblog, half of which was in Chicago for another forum, so links to some pictures/commentary below as well.
Pizza - I've only tried Lou Malnati's and Original Unos, but Lou Malnati's was much better .
http://egullet.org/p1823818Hot Dogs - Hot Doug's is the "original" for crazy and delicious hot dogs, but last trip we went to Franks and Dawgs in Lincoln Park and I thought it was as good or better (and you don't have to stand in line)
http://egullet.org/p1824136Italian Beef - If you haven't tried this sandwich, it is quite good. We went to Mr. Beef but there are plenty of options (Portillo's you can get good Italian Beef and Chicago style dogs)
Rick Bayless - I think Xoco (his fast casual place) is probably the overall most enjoyable of the three - breakfast or lunch.
http://egullet.org/p1823940If you like beer, Publican in the West End has great food and awesome beer selection. (No pictures but had great dinner in September 10). Had a great meal last trip at the Purple Pig, which is more casual small plates and delicious
http://egullet.org/p1824040If you are going to have a car and are at all interested in Polish, highly recommend Smak Tak (it's a ways out of town but more or less on the way to the airport).
http://egullet.org/p1824141 My wife is half polish and we've eaten quite a bit of Polish food (including in Poland) and this was probably the best.
I've spent a lot of time doing research, so if you have other wants I can probably at least point you in the direction of something. All of the above are near central Chicago except Smak Tak and Hot Doug's
In terms of activities - the Shedd aquarium was excellent, Lincoln Park Zoo was fun (and free), and highly recommend the Chicago Architecture Foundation boat tour.
Hotels - I've had very good luck getting deals on Hotwire for $100 or so off of the best published rate at pretty nice places.