I live in Chicago where Intelligentsia was started and has several locations. Intelligentsia is good coffee but it's not the best in town by any means. Other strong (Chicago based) competitors:
I haven't been to any of their Chicago locations, just Venice and Silver Lake in LA. I was also at a cafe in Tokyo a few weeks ago that imports Intelligentsia, which personally seems like overkill.
http://www.halfwitcoffee.com/
http://www.bigshoulderscoffee.com/
http://gaslightcoffeeroasters.com/
http://www.lacolombe.com/
http://www.darkmattercoffee.com/