Not sure if you are looking for a venue right in the city or if you would consider expanding your borders to the suburbs.
Here are a few suggestions from lil' ol' me:
Chicago - city
Subterranean
http://www.subt.net/
I haven't been here in probably two years, but last time I was there, I enjoyed it a lot. Very dark atmosphere ( \m/ ), open floor plan, lots of room, decent stage, upstairs loft with a bar, couches and chairs to hang out.
I honestly do not remember how great the sound was, but it must not have been that bad becuase if it was, I surely would have remembered.
The Kinectic Playground
http://www.thekineticplayground.com/
This would be my second choice. Same open floor plan, couches and 'lounge area' against back wall.
Sound is okay in this place. FREE PARKING!
Chicago suburbs
JJ Kelly's
Lansing
The only thing bad I can say about this place is it is so...far...away! Unless you live on the border of IL/IN, that is.
I've never had a bad experience here. It's a smaller venue, but the sound is good, they updated the stage area within the past year, reasonable prices on drinks, back patio. They really need to get rid of the banquet hall-type tables in front of the stage. It's a concert! Get your asses up!
Chicago City Limits
-Schaumburg
Aside from the fact that it has the look and feel of a sports bar, this place is pretty cool. I have seen such acts as WASP, John Oliva's Pain, Bret Michaels and Skid Row here. The sound is good, the stage is okay, and there is an ample amount of room in front of the stage (the bar is about 10 or 15 feet from the front of the stage, but if they got rid of the tables Stage Left, there would be a lot more room for standing).
Austin's Fuel Room
-Libertyville
This is an awesome room. Great stage! However, this venue is mostly known for cover bands, unless Bret Michaels is in town. Ha Ha!