Love Jack-In-the-Box.
Chick-fil-A is one of my favorites and as far as I know they don't have it in the Midwest.
So many places have been going national over they years. I remember when Iowa City got it's first Wendy's, Hardees (they used to have this great breaded tenderloin sandwhich), Long John Silvers.
Where I lived in Bettendorf got it's first Taco Bell back in 1987. Before that the closest ones were in Chicago.
One chain that I still only see in the midwest is Godfather's Pizza. It's pretty decent and was rather big when I was a kid.
On the really small chain front: Happy Joe's Pizza and Ice Cream Parlor. When I was a kid they had them in at least the Quad Cities and Iowa City but I don't know if they still exist or if they were spread out any further than that.
How about Shakey's Pizza? I know they at least used to have them in Iowa and I ate at one in the early 90's in California, so are they still around and in what parts of the country?
One place I like that I've only seen in Florida is Crystal Burgers. Little nasty burgers, and dogs. I absolutely love the chilli cheese pups but don't look too closely at them.

Sonic - we have the drive in versions here in Arizona.
Steak and Shake - Saw those back in Iowa and the midwest this summer but as far as I know we don't have them here. From what I recall the couple times I ate at one (20+ fucking years ago) they were pretty good. People who like shakes seem to really like them. IIRC their hamburgers were a little more meat tasting than most of the burger chaings at the time.
York Steak House - I don't think they exist anymore but they were right up my alley. It was a walk in walk through the line steak place. I think you still had to sit down for a few minutes while they flash fried your steak but it was faster and cheaper than going to a place with a waiter. Those were only in the midwset that I can remember.