not exactly setting the world on fire with wine options at restaurants. I've been trying to think of a reply to this thread for a few days now and after talking about the state of restaurant lists in Chicago with a few people, I have come to the (not-so-definite) conclusion that while you can find something good to drink at most of the decent restaurants, the most exciting lists in town are at the wine bars. Webster's Wine Bar and Rootstock in particular. Both places you can get food at if so inclined (the burger at Rootstock is tasty). Of course you're going to get your tonied, prize lists at L2O and Trotter's and Alinea (where evidently most go for the pairings [which has included Sine Qua Non but also Magma] as opposed to ordering off the list). One of the best lists (but priced to match) is at Spiaggia. The wine director there is given a good deal of autonomy and brings in some exciting things (just wish I could afford to go there). If you're rolling in with an expense account, might want to check it out.
There have been quite a few places opening up within the last six months or so but I'm a little partial to particular neighborhoods and areas. Much like some not going above 14th St in New York, I don't venture up to the North side of the city very often (and avoid Wrigleyville like the plague).
Places I can recommend (because I've been there and like them):
Avec (Paul Kahan tapas-y place)
Publican (Paul Kahan farm to table place)
Big Star (Paul Kahan tacos and beer place)
Longman & Eagle (meaty meat meat place in Logan Square)
Nightwood (farm to table in Pilsen)
Birreria Reyes de Octolan (insane goat's head tacos in Pilsen)
Xoco (Bayless empire)
Frontera (Bayless empire)
Mana (great vegetarian)
Green Zebra (fancier vegetarian)
Schwa (incredible BYO)
Belly Shack (owners of Urban Belly's Korean style sandwich place)
Irazu (Costa Rican BYO)
Naha (fancy business-y good for lunch)
Lula Cafe (Monday night farm dinner is a good deal)
West Town Tavern (straight forward nothing fancy but good; tasty fried chicken)
Hot Dougs (stand in line. it's worth it. esp the weekend duck fat fries)
Purple Pig (MI Ave. Just had lunch there. Fucking tasty. Again list is going to set hearts aflame, but they do have Lopez Heredia stuff. Great for lunch.)
Places that are supposed to be good or getting buzz (but I haven't been to yet):
Bristol
Revolution Brewing
Salpicon
Urban Belly
Alinea, Trotter's, L2O, etc.
That should keep you busy for a while. Use that Google site for more info. I'm sure I've forgotten a few places, like Mado which is good but not great. Also, do yourself a favor and try to hit an old-man, corner bar (we've got a few). I recommend Richard's (in my neighborhood).
Oh yeah, wine stores in case you go to a BYO:
Perman Wine (West Loop; my preferred joint)
Red & White (Wicker Park)
Binny's (throw a rock and you should hit one)
Lush (there's a couple)
Howard's Wine Cellar (um, not sure of the 'hood; North)