if baseball is playing, The Cell to see the White Sox is a must
My son and his friends call Lincoln Park Zoo the Animal Torture Zoo, due to the small cages.
I like the Museum of Science and Industry, but if you're only going for a weekend, I'd skip it, because there's so much to see inside you'll kill a whole day. I'd only go if it's raining. I was mugged and had my lunch money stolen on a sixth grade field trip inside the giant walkthrough heart, but don't let that stop you from going.
The boat tours on the river are a great way to see the city.
If you're strolling Michigan Avenue, stop in the Billy Goat Tavern for a "cheeseburger cheeseburger" or maybe just a cold Old Style.
For breakfast, find the nearest Ann Sather. http://www.annsather.com/
Cinnamon rolls to die for.
For dinner, it has to be pizza. Gino's East was my favorite in my younger days, but Giordano's good too, and just naming places usually starts an argument.
Second City is great for late night comedy.