What kind of museum do you like? Any of them are good, but my personal favorite is the Museum of Science and Industry. Also available are the Art Institute (awesome, but I've been there too many times), Field Museum, Shedd Aquarium, and Adler Planetarium. The last three are right next to each other.
I personally don't care for the deep-dish Chicago pizza, so I won't give my opinion there because its not an educated one. But yes, it is Gino's East.
Do you like architecture? Take a Chicago River architecture tour: http://www.chicagoline.com/schedule.php. I really enjoyed this, a nice few hours floating down the river learning about all the buildings. I believe you can also purchase overpriced alcohol on board.
What kind of food do you like? BBQ? Steak? Polish? Italian? Greek? Jewish? You name it, there is a good one there, and I know of a few good ones personally. But two places that I've never been to, and really want to based on everything I hear, are Carnivale, and Fogo de Chao. If you want a truly excellent meal, go to one of these places. Otherwise I could recommend my personal favorites, but they are mostly on the far north side.
What about music? Old Town School of Folk Music is always a cool place to visit. Numerous blues and jazz places as well.
Somewhere on Michigan Avenue they have horse carriage rides, if you're into that stuff.
Second City comedy club is always a good bet. Your sides will probably be hurting by the end of it.
Two zoo's, haven't been to either one since I was 10, but both are good. I guess... Lincoln Park Zoo and Brookfield Zoo.
Chicago Shakespeare theater is on Navy Pier, always can catch a good show there.
Anything else I think of I'll post later, but this is it for now. I really only spend a day or two a year in Chicago, and thats usually for Cubs and Blackhawks games. Oh, and of course the Autoshow if I can make it. The girlfriend and I will go ice skating at Millennium park, but thats out for October.