I moved to chicago in September, and living on the south side all the shops are pretty far so I've hit a bunch of them.

Yay:
-Yojimbo's (duh)
-Boulevard (again, duh. Best experience I've ever had in a shop and I wanted to like bake them cookies or something when I didn't end up spending money there)
-Turin (carry some lines others don't, but turbo-far. Worth the trip if you're buying a frame or complete, tho)
-Rapid Transit
-Uptown
-Performance (yeah, they're big and corporate, but everybody who works there is cool, including the manager, and they know their stock. Good selection and cheap if you need clothes/shoes)
-Art's Cycle (Hyde Park. OK local shop, kind of Soviet - they have one and only one option for everything, take it or leave it.)

Boo That Ish:
-Village (They seem to hire some people who don't know bikes)
-Wheels & Things (Hyde Park. Certifiable Hole. Owner is a jackass, could give any shop a run for its money as worst LBS.)
-Kozy (Not sure why so many people like this place, but I went to the one next to the Lincoln Park Ballys back when I didn't know better. Good mechanics I hear, jury's still out I guess.)