Great thread to revive.
The Flying J at exit 125 on I35/80 on the west side of Des Moines, IA has a lousy restaurant, but serve some very good items up at the counter in the convenience store. Their gizzards are worth a lunch trip from Minneapolis alone (well...for me at least). Kept "fresh", hot, crunchy and spicy -- gizzard gnawing heaven! They also do something I previously thought possible with a "bagel dog" (hot dog wrapped in a bagel-like casing). Not only is it, literally, a 20 ounce hot dog (in itself no small feat), but it also was very good quality. You really have to like hot dogs though. I haven't seen a hot dog that obscenely large since the Slots O' Fun's $0.99 giant in Las Vegas. Their pizza by the slice is also good. Yes, I ate all three items in one visit two weeks ago.
Johnson's Corner near Loveland, CO (Exit 254 on I-25) is also legendary. www.johnsonscorner.com
Monstrous cinnamon rolls and good burgers.
I recently stopped in the Ambest truck stop (aka "Shoemakers Truck Station) west of Lincoln, NE (exit 395 on I-80). The restaurant there is good and if you're a collector of die cast trucks, NASCARs or farm equipment, they had a pretty impressive array.
I also enjoy the Clearwater Travel Plaza in Clearwater, MN (exit 178 on I-94) but for a little more "upscale" truck stop food. This is actually my healthy alternative to fast food on the way "up north". They have an in-house bakery and make very good cold cut sandwiches to order on several types of bread. Choose from a zillion different options. The other baked goods (cinnamon rolls, pies, etc.) are also very good and they have about 10 different coffees at any given time as well as good soups. Skip the sit-down restaurant.
Finally, I concur with the commentary on "chain" truck stops (vary greatly with location), as well as the Bosselman mention (at least in Nebraska, these were very clean facilities...good options).