As others have mentioned, there are probably too many to list, so a good place to start is with what kind of restaurant you prefer. If you want someplace super-casual, you might be interested in the Billy Goat Tavern or Hot Doug's. If you want upscale Italian, there's Spiaggia, for instance, which has long been considered one of the finest Italian restaurants in the U.S. For something more unique, try Alinea or (if you can get tickets) Next.
So much depends on your preferences and tastes, so a good place to start is a site like Yumbly.com that lets you search by exactly what you like to eat, and then of course Yelp for lots more reviews by other diners.